DE-N-Acetyl Sialic Acid Antigens, Antibodies Thereto, and Methods of Use in Cancer Therapy

ABSTRACT

The present invention generally provides compositions methods and composition relating to the diagnosis and/or treatment of cancers having a cell surface de-N-acetylated sialic acid antigen, e.g., an at least partially de-N-acetylated ganglioside and/or a de-N-acetylated sialic acid-modified cell surface protein.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority benefit of U.S. provisional applicationSer. No. 60/753,847, filed Dec. 23, 2005, and is a continuation-in-partof U.S. application Ser. No. 11/166,781, filed Jun. 23, 2005, whichapplication claims priority benefit of U.S. provisional application Ser.No. 60/582,672, filed Jun. 23, 2004, which applications are eachincorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under grants no. AI46464and AI45642 awarded by the National Institute of Allergy and InfectiousDiseases, and the National Institute of Health. The government may havecertain rights in this invention.

BACKGROUND OF THE INVENTION

In general, the goal of anti-cancer immunotherapy has been to identifystable antigens that are highly expressed but not shed or secreted fromtumor cells, which antigens can then be used as the basis ofimmunotherapy, e.g., as the antigen in a cancer vaccine or as a targetfor antibody-based cancer therapy. Optimally, such tumor antigens wouldalso be ones that elicit an immune response that is acceptably specificfor the cancerous target cells, so as to reduce deleterious side effectsthat can result from cross-reactivity with non-cancerous cells of thesubject being treated. Where cross-reactivity affects cells that can berepopulated, it may be acceptable to relax this requirement for thespecificity of immunotherapy.

For example, although other antibodies are available for use in treatingleukemias/lymphomas, the current standard for monoclonal antibody (mAb)therapy of non-Hodgkins lymphoma is RITUXIMAB™, a chimeric murine/humanmAb that recognizes CD20 antigen. CD20 is highly expressed in mostmature B cells and B-cell lymphomas, exhibits relatively slow modulationof expression or antigenic determinants, and is not shed or secreted.Although this antibody also binds CD20 on non-cancerous B cells, thiscell population can be restored, e.g., through supportive treatment withimmune enhancing therapeutics such as granulocyte-macrophagecolony-stimulating factor (GM-CSF), erythropoietin (EPO), etc. Fcregions of antibodies binding to cell surface antigens can mediatecomplement deposition and cell lysis (complement dependent cytotoxicityor CDC) or antibody-dependent cellular cytotoxicty (ADCC) by activatingnatural killer (NK) cells. Although not as common, antibodies can alsobe cytotoxic by binding to cell surface antigens that affect a signalingpathway leading to apoptosis. For example, although the mechanism ofaction of RITUXIMAB™ is not completely understood, it appears to exertits cytotoxic effects on CD20-positive tumor cells by a combination ofantibody-dependent CDC, ADCC, and by activating cellular signalingpathways that lead to apoptosis. With the success of Rituximab, severalother cellular antigens have been targeted with mAbs including CD22,CD30, and CD80.

In addition to passive immunotherapy through antibody administration,several active immunization strategies have also been explored.Exemplary cancer vaccines involve administration of a tumor antigen soas to elicit humoral antibody and/or cellular immune responses that areable to activate complement, and opsonophagocytotic killing of tumorcells. Exemplary vaccine compositions include those based on tumor celllysates, and tumor-specific antigens (e.g., proteins, gangliosides (Tai,T., et al. Int J Cancer, 1985. 35:607-12) , anti-idiotype immunoglobulin(Ig), etc. (Foon et a 1. J Clin Oncol, 2000. 18: 376-84) or peptidefragments of tumor-specific or overexpressed proteins that are derivedfrom non-autologous and autologous cancers of the same type (Morioka etal. J Immunol, 1994. 153: 5650-8; Morioka, N., et al., Mol Immunol,1995. 32: p. 573-81).

One limitation of these approaches has been that, although the targetantigens are typically more highly expressed in tumor cells, they arenonetheless autoantigens and, thus, poorly immunogenic. Thus, cancervaccines often employ various strategies for enhancing immunogenicity ofthe cancer antigen, e.g., combination with adjuvants, administrationwith a cytokine(s), linkage to to carrier proteins, and use inpulse-activation of mature dendritic cells in vitro. A more recent trendhas been to develop more elaborate vaccination strategies that aretailored to the patient in which autologous dendritic cells areisolated, stimulated with tumor lysates or peptides and reinjectedeither alone or in combination with potent immunostimulatory cytokines(e.g., GM-CSF, interleukins IL-2 and IL-12, interferon gamma).

SUMMARY OF THE INVENTION

The present invention generally provides compositions methods andcomposition relating to the diagnosis and/or treatment of cancers havinga cell surface de-N-acetylated sialic acid antigen, e.g., an at leastpartially de-N-acetylated ganglioside and/or a de-N-acetylated sialicacid-modified cell surface protein.

The disclosure provides various aspects of the invention. These includethe following exemplary embodiments.

In one embodiment, methods of inhibiting growth of a cancerous cell areprovided, which methords comprise administering to a subject apharmaceutically acceptable formulation comprising an antibody thatspecifically binds a de-N-acetylated sialic acid (deNAc SA) epitope onan extracellularly accessible surface of a cancerous cell present in thesubject, wherein administering facilitates reduction in viability ofcancerous cells bound by the antibody. In related embodiments, the deNAcSA epitope is presented on a surface of the cancerous cell during celldivision. In further related embodiments, the cancer is a melanoma, aleukemia, or a neuroblastoma. The antibody can be administered byinfusion or by local injection, and can be administered prior, at thetime of, or after surgical intervention to remove cancerous cells. Theantibody can also be administered as part of a combination therapy, inwhich at least one of a cancer chemotherapy or a radiation therapy isadministered to the subject.

In another embodiment, methods of inhibiting growth of a cancerous cellin a subject are provided which methods comprise administering to asubject a pharmaceutically acceptable formulation comprising an antibodythat specifically binds a SEAM-3 reactive antigen on an extracellularlyaccessible surface of a cancerous cell present in the subject, whereinadministering facilitates reduction in viability of cancerous cellsbound by the antibody. In related embodiments, the SEAM 3 reactiveantigen is presented on a surface of the cancerous cell during celldivision. In further related embodiments, the cancer is a melanoma, aleukemia, or a neuroblastoma. The antibody can be administered byinfusion or by local injection, and can be administered prior, at thetime of, or after surgical intervention to remove cancerous cells. Theantibody can also be administered as part of a combination therapy, inwhich at least one of a cancer chemotherapy or a radiation therapy isadministered to the subject. In one related embodiment, the antibody isa SEAM 3 monoclonal antibody (ATCC Deposit No. HB-12170). In a furtherrelated embodiment, the SEAM 3 monoclonal antibody has been isolatedusing a high salt concentration step, in which a composition comprisinga SEAM 3 monoclonal antibody is incubated in a high salt concentrationsolution under conditions suitable to facilitate separation of chargedmolecules from the SEAM 3 mAb in the solution. The SEAM 3 mAb isisolated from this solution, usually by removing precipitates andfurther isolating the mAb.

In another embodiment, methods of eliciting antibodies to a cancerouscell in a subject are provided, which methods comprise administering toa subject an immunogenic composition comprising a de-N-acetylated sialicacid (deNAc SA) antigen and an adjuvant, wherein the subject has or issuspected of having a cancer characterized by a de-N-acetylated sialicacid (deNAc SA) antigen, where such administration is effective toelicit production of an antibody that specifically binds a deNAc SAepitope on an extracellularly accessible surface of a cancerous cell. Inrelated embodiments, the cancer is a melanoma, lymphoma, or leukemia, orneuroblastoma. In further related embodiments, the deNAc SA antigen ofthe immunogenic composition is prepared by exosialidase treatment ofdeNAc SA antigen. In still further related embodiments, the deNAc SAantigen is a deNAc SA antigen conjugate, which can be, for example, apropionyl-linked or acetyl-linked deNAc SA antigen conjugate.

In another embodiment, methods of detecting a tumor in a subject areprovided, which methods comprise contacting a biological sample obtainedfrom a subject suspected of having cancer with an antibody thatspecifically binds a de-N-acetylated sialic acid (deNAc SA) epitope,where contacting is under conditions suitable for specific binding ofthe antibody to a deNAc SA epitope in the biological sample, thepresence or absence of binding of the antibody is indicative of thepresence or absence of cancerous cells having a cell surface deNAc SAepitope in the subject.

In another embodiment, methods of detecting a tumor in a subject areprovided, the which methods comprise contacting a biological sampleobtained from a subject suspected of having cancer with an antibody thatspecifically binds a SEAM 3 reactive antigen, said contacting beingunder conditions suitable for specific binding of the antibody to a SEAM3 reactive antigen in the biological sample, where the presence orabsence of binding of the antibody is indicative of the presence orabsence of cancerous cells having a cell surface SEAM 3 reactive antigenin the subject. In related embodiment, the antibody is the SEAM 3monoclonal antibody (ATCC Deposit No. HB-12170).

In another embodiment, methods of producing a polysaccharide (PS)derivative that is a suitable deNAc SA antigen are provided, whichmethods comprise culturing an Escherichia coli K1 bacterium in a growthmedium comprising an N-acyl-mannosamine and an amine-protectedmannosamine, wherein the bacterium is deficient in production of capsulepolysaccharide in the absence of supplemental mannosamine, where theculturing provides for production of an amine-protected PS derivativehaving an amine protecting group and an N-acylated group. In relatedembodiments, method also includes treating the amine-protected PSderivative under conditions to remove the amine protecting group andcouple the deprotected residue to a protein carrier to produce aconjugated PS derivative.

In another embodiment, methods of producing a deNAc SA antigen areprovided, which methods comprise culturing a mammalian cell in a growthmedium comprising an N-acyl-mannosamine and an amine-protectedmannosamine, where the culturing provides for production of anamine-protected deNAc SA antigen having an amine protecting group and anN-acylated group on the surface of the mammalian cell. In relatedembodiments, the method also includes treating the amine protected deNAcSA antigen under conditions to remove the amine protecting group andcouple the deprotected residue to a protein carrier to produce aconjugated deNAc SA antigen. Amine-protected deNAc SA antigens producedby this method are also provided, as are mammalian cells having a cellsurface deNAc SA antigen produced by this method, and membrane and lipidextracts of such mammalian cells.

In another embodiment, methods of producing an immunogenic compositionsare provided, which methods comprise contacting a composition comprisinga de-N-acetylated sialic acid (deNAc SA) antigen with an exosialidase,said contacting being under conditions sufficient to provide fordegradation of N-acylated sialic acid polymer contaminants in thecomposition, where the contacting produces a deNAc SA antigen-enrichedcomposition. Compositions comprising deNAc SA antigen prepared by thisexosialidase treatment method are also provided.

In another embodiment, methods of isolating an anti-deNAc SA epitopeantibody and methods of isolating a SEAM 3 monoclonal antibody areprovided, where such methods comprise incubating a compositioncomprising the antibody in a high salt concentration solution, saidincubating being under conditions suitable to facilitate separation ofcharged molecules from the SEAM 3 mAb in the solution, and isolating theSEAM 3 mAb from the solution. Also provided are compositions comprisingan anti-deNAc SA epitope antibody and a pharmaceutically acceptablecarrier, where the antibody is isolated by this method. Also providedare compositions comprising a SEAM 3 monoclonal antibody and apharmaceutically acceptable carrier, where the antibody is isolated bythis method.

In another embodiment, isolated polynucleotides are provided, whichpolynucleotides comprise a nucleotide sequence encoding a light chainpolypeptide comprising i) amino acid residues 24 to 39, ii) amino acidresidues 55 to 61, and iii) amino acid residues 94 to 100 of a variableregion of a SEAM 3 light chain polypeptide. In related embodiments, theencoded light chain polypeptide comprises the amino acid sequence of thevariable region of a SEAM 3 light chain polypeptide. In further relatedembodiments, vectors and recombinant host cells containing suchpolynucleotides are provided.

In another embodiment, isolated polynucleotides are provided, whichpolynucleotides comprise a nucleotide sequence encoding a heavy chainpolypeptide comprising i) amino acid residues 26 to 35, ii) amino acidresidues 50 to 66, and iii) amino acid residues 101 to 108, of avariable region of a SEAM 3 heavy chain polypeptide. In relatedembodiments, the encoded heavy chain polypeptide comprises the heavychain polypeptide comprises the amino acid sequence of the variableregion of a SEAM 3 heavy chain polypeptide. In further relatedembodiments, vectors and recombinant host cells containing suchpolynucleotides are provided.

In another embodiment, antibody conjugates are provided, where theantibody conjugates comprise an antibody comprising antigen-bindingportion of a SEAM 3 monoclonal antibody (ATCC Deposit No. HB-12170), anda covalently bound moiety, where the covalently bound moiety is apolyethylene glycol moiety, an anti-cancer drug, or an antigen-bindingportion of an antibody. In related embodiments, the antibody of theconjugate is a SEAM 3 monoclonal antibody.

Other features of the invention will be readily apparent to theordinarily skilled artisan upon reading the disclosure herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides the structure of NmB PS following de-N-acetylationaccording to the invention. R is H on most residues to provide a freeamine (on a deacetylated group). In a small fraction of residues in thede-N-acetylated product, R may be CH₃C═O (an acetyl group). “n”represents a number of sialic acid residues in the polymer, which mayhave the value of “n” in other formulae described herein.

FIG. 2 provides the structure of a lactone moiety formed between the Clcarboxyl group and the C9 hydroxyl group of the preceding residue in NmBPS following acid treatment of NmB PS.

FIG. 3 provides the structure of a PS derivative having an aldehydegroup at the non-reducing end terminal residue.

FIG. 4 shows the mass spectrum of PS derivatives selected and protectedfrom neuraminidase cleavage by SEAM 3.

FIG. 5 is a table summarizing the observed masses for each sample andtheoretical masses of corresponding ions that are consistent with theobserved masses.

FIGS. 6-15 provide structures of de-N-acetylated PS derivativesidentified in FIG. 5.

FIGS. 16-18 provide structures of dodecylamine NmB PS derivativesprepared and identified in EXAMPLE 1.

FIGS. 19-33 provide structures of exemplary acyl amine de-N-acetylatedPS derivatives of the invention.

FIG. 34 is a table summarizing the results of binding of the SEAM mAbs2, 3, 12, 18 and 35 to dodecylamine NmB PS derivatives as measured bydirect binding ELISA. The mAb SEAM 3 is described in U.S. Pat. No.6,048,527. ^(a) Concentration of mAb in micrograms/ml required to givean OD405 nm equal to 0.5 in 1 hr by ELISA with the non-reducing enddodecylamine NmB PSderivative coated on the plate and the bound mAbdetected using goat anti-mouse IgG, M, A alkaline phosphatase conjugatesecondary antibody as described in the text. ^(b)Preparation andcomposition of NmB PSderivatives are as described in the text. Colominicacid was used to prepare this derivative. Since the colominic acid isfrom an E. coli K1 strain that does not O-acetylate the hydoxyl groupson C7 and C9, the polysaccharide is chemically identical tomeningococcal group B polysaccharide (NmB PS). N—Pr, N-propionyl; N—Ac,N-acetyl; OS oligosaccharide; PS, polysaccharide; Dp, degree ofpolymerization.

FIG. 35 is a table summarizing the results of binding of the SEAM mAbs2, 3, 12, 18 and 35 to BSA-NmB PS derivative conjugates as measured bydirect binding ELISA. The mAb SEAM 3 is described in U.S. Pat. No.6,048,527. ^(a)Concentration of mAb in micrograms/ml required to give anOD405 nm equal to 0.5 in 1 hr by ELISA with the non-reducing end BSA NmBPS derivative coated on the plate and the bound mAb detected using goatanti-mouse IgG, M, A alkaline phosphatase conjugate secondary antibodyas described in the text. ^(b)Preparation and composition of NmBPSderivatives are as described in the text. Colominic acid was used toprepare this derivative. Since the colominic acid is from an E. coli K1strain that does not O-acetylate the hydoxyl groups on C7 and C9, thepolysaccharide is chemically identical to meningococcal group Bpolysaccharide (NmB PS). N—Pr, N-propionyl; N—Ac, N-acetyl; OSoligosaccharide; PS, polysaccharide; Dp, degree of polymerization.

FIG. 36 is a chromatogram from high performance anion exchangechromatography of colominic acid (i.e. poly alpha (2→8) N-acetylneuraminic acid prepared from E. coli K1) (curve number 1) and N—Pr NmBPS that had been exhaustively treated with sialidase A

FIG. 37 is panel of photographs illustrating binding of SEAM 12 to NmBstrain M7 in which the growth media was supplemented with N-acylmannosamine derivatives as measured by fluorescence microscopy. Leftpanel: binding of SEAM 12 mAb to M7 supplemented with N-acetylmannosamine; Left middle panel: binding of SEAM 12 to M7 without N-acylmannosamine supplement; Right middle panel: binding of SEAM 12 mAb withN-trichloroacetyl mannosamine supplement; Right panel: binding of mAbSEAM 12 to the capsule PS containing N-trifluoroacetyl groups. The mAbSEAM 12 is described in U.S. Pat. No. 6,048,527.

FIG. 38 is a photograph showing the reactivity of an anti-de-N-acyl GD3mAb, GAG2, and SEAM 3 with de-N-acetyl sialic acid gangliosides preparedchemically or biosynthetically. The ganglioside derivatives wereseparated by high performance thin layer chromatograpy and detected byWestern blot with either GAG2 (Lanes 1-3) or SEAM 3 (Lanes 4-6).

FIG. 39 is a series of photographs of human normal and melanoma cancertissues depicting the immunohistochemical analysis of SEAM 3 andanti-GD3 mAb, R24 binding.

FIG. 40 is a table summarizing the results of immunohistochemicalanalysis of SEAM 3 binding to a panel of human cancers.

FIG. 41 is a photograph showing fluorescence binding of SEAM 3 to SK-MEL28 melanoma cells (dark shading).

FIG. 42 is a photograph showing fluorescence binding of SEAM 3 toCHP-134 neuroblastoma cells (dark shading).

FIG. 43 is a photograph showing fluorescence binding of SEAM 3 to JurkatT-cell leukemia cells (dark shading).

FIG. 44 is a set of graphs showing binding of SEAM 3, anti-GD3 mAb R24,and an irrelevant istotype-matched control mAb to SK-MEL 28 melanomacells in the absence and presence of Triton X-100.

FIG. 45 is a set of graphs showing binding of SEAM 3, anti-NCAM mAb, andirrelevant istotype-matched control mAbs to CHP-134 neuroblastoma cellsin the absence and presence of Triton X-100 by flow cytometry.

FIG. 46 is a set of graphs showing binding of SEAM 3 and an irrelevantistotype-matched control mAb to Jurkat cells in the absence and presenceof Triton X-100 and the soluable polysaccharide inhibitor, N—Pr NmB PSby flow cytometry.

FIG. 47 is a graph showing the decrease in cell viability of SK-MEL 28melanoma cells after incubation of cells in the presence of 5 μg/ml ofSEAM 3 for 24 h.

FIG. 48 are graphs comparing the decrease cell viability and increase inthe number of apoptotic and dead SK-MEL 28 melanoma cells afterincubation of cells in the presence of 5 μg/ml of SEAM 3, anti-GD3 mAb,R24, or an irrelevant istopye-matched control mAb for 48 h.

FIG. 49 are graphs showing the shift of SK-MEL 28 melanoma cells to preGo in the presence of SEAM 3 compared to the effects of the drugnocodozole and the anti-GD3 mAb R24.

FIG. 50 is a scatter plot comparing the percentage of SK-MEL 28 cellsexpressing SEAM 3-reactive antigen and the cell proliferation markerKi67.

FIG. 51 is a table showing a comparison of the genetic origin ofvariable regions of anti-MBPS and anti-N—Pr MBPS mAbs. 2 Closest matchesfrom either the IGMT or GenBank/EMBL databases. MAb 735 is from ahybridoma produced from a NZB mouse immunized with viable N.meningitidis group B strain ATCC 13090 (Frosch et al. (1985) Proc NatlAcad Sci USA 82, 1194-8). Since only the amino acid sequences werereported (Klebert et al. Biol Chem Hoppe Seyler 374, 993-1000; Vaesen etal. (1991) Biol Chem Hoppe Seyler 372, 451-3), assignment of thegermline genes for this mAb was based on the closest match (see Methodssection). MAb 2-2-B was produced from a BALB/CJ mouse immunized with N.meningitidis group B strain P355. Germline assignments were based on thepublished DNA sequences (Berry et al. (2005) Mol Immunol 42, 335-44).The SEAM mAbs are from hybridomas prepared from CD1 mice immunized withN—Pr NmB PS tetanus toxoid conjugate (Granoff et al., 1998). ^(b)ND, notdetermined since the segment was too short to enable identification of aspecific gene. ^(c)This mAb was previously listed as being IgG2b, buthas subsequently been confirmed to be IgG2a. The subclasses of all ofthe other anti-N—Pr NmB PS mAbs used in this study were retested andconfirmed as listed here and in (Granoff et al. (1998) J Immunol 160,5028-36).

FIG. 52 is a schematic showing a comparison of V_(L) and V_(H) sequencesfor mAb 735 and SEAM mAbs. Boxed segments correspond to complementaritydetermining regions (CDR) loops. GenBank accession numbers: SEAM 2 VH,DQ113489 (SEQ ID NO:13); SEAM 2 VL, DQ113490 (SEQ ID NO:3); SEAM 3 VH,DQ113491 (SEQ ID NO:7); SEAM 3 VL, DQ113492 (SEQ ID NO:3); SEAM 12 VH,DQ113493 (SEQ ID NO:10); SEAM 12VL, DQ113494(SEQ ID NO:5); SEAM 18 VH,DQ113495 (SEQ ID NO:8); SEAM 18 VL, DQ113496 (SEQ ID NO:6); SEAM 35 VH,DQ113497 (SEQ ID NO:9); SEAM 35 VL, DQ113498 (SEQ ID NO:4). FIG. 52 alsoprovides amino acid sequences of the mAbs 735 VL (SEQ ID NO:1); 735 VH(SEQ ID NO:11); 2-2-B VL (SEQ ID NO:2); and 2-2-B VH (SEQ ID NO:12).

FIG. 53 is a schematic showing the nucleic acid (SEQ ID NO:15) and aminoacid sequences (SEQ ID NO:14) of the heavy chain polypeptide of SEAM3.

FIG. 54 is a schematic showing the nucleic acid (SEQ ID NO:17) and aminoacid sequences (SEQ ID NO:16) of the light chain polypeptide of SEAM3.

FIG. 55 is a table showing a comparison of assigned germline gene andamino acid sequences to respective expressed sequences for anti-NmB PSand anti-N—Pr NmB PS mAbs. ^(a)Percent identity as calculated frompairwise CLUSTALW alignments. The sequence comparison does not includeresidues determined by the primers used to amplify and clone the genesequences. ^(b)From (Berry et al., 2005). From (Klebert et al., 1993;Vaesen et al., 1991). ^(d) The gene sequences are unknown. Theidentification of germline sequence is based on comparison of the aminoacid sequence with the sequences in the IMGT/V-QUEST database.

FIG. 56 is a schematic showing the relationship of the DNA sequences ofthe SEAM3 light chain (SEQ ID NO:18) to variable region framework andCDRs as defined by International Immunogenetics Information System(IMGT) definitions (Lefranc et al. IMGT, the internationalImMunoGeneTics information system®. Nucl. Acids Res., 2005, 33,D593-D597).

FIG. 57 is a schematic showing the relationship of the DNA sequences ofthe SEAM3 heavy chain (SEQ ID NO:19) to variable region framework andCDRs as defined by International Immunogenetics Information System(IMGT) definitions (Lefranc et al. IMGT, the internationalImMunoGeneTics information system®. Nucl. Acids Res., 2005, 33,D593-D597).

FIG. 58 is a schematic showing the relationship of the DNA sequences ofthe SEAM3 heavy chain to variable region D and J (SEQ ID NO:20) chainsas defined by International Immunogenetics Information System (IMGT)definitions (Lefranc et al. IMGT, the international ImMunoGeneTicsinformation system®. Nucl. Acids Res., 2005, 33, D593-D597). The DNA(SEQ ID NO:22) and amino acid (SEQ ID NO:21) sequences of the DJjunction are also provided.

Before the present invention and specific exemplary embodiments of theinvention are described, it is to be understood that this invention isnot limited to particular embodiments described, as such may, of course,vary. It is also to be understood that the terminology used herein isfor the purpose of describing particular embodiments only, and is notintended to be limiting, since the scope of the present invention willbe limited only by the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges is also encompassed within the invention, subject to anyspecifically excluded limit in the stated range. Where the stated rangeincludes one or both of the limits, ranges excluding either both ofthose included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present invention, exemplarymethods and materials are now described. All publications mentionedherein are incorporated herein by reference to disclose and describe themethods and/or materials in connection with which the publications arecited.

It must be noted that as used herein and in the appended claims, thesingular forms “a”, “and”, and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “anantigen” includes a plurality of such antigens and reference to “thepeptide” includes reference to one or more peptides and equivalentsthereof known to those skilled in the art, and so forth.

The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed.

DETAILED DESCRIPTION OF THE INVENTION

The de-N-acetyl sialic acid (deNAc SA) antigen compositions disclosedherein are useful in cancer immunotherapy as well as in production ofantibodies that can be used in antibody-based cancer chemotherapy.Accordingly, the disclosure provides deNAc SA antigens, as well asmethods of their use in eliciting an anti-tumor immune response and/orenhancing an anti-tumor immune response, where the tumor contains cellshaving cell surface accessible deNAc SA antigen.

In general, deNAc SA antigens contain de-N-acetyl sialic acid residuesthat, following administration to a subject, can elicit antibodies thatspecifically bind deNAc SA epitopes on a cancer cell. In someembodiments, the deNAc SA antigen provide for an antibody response thathas minimal cross-reactivity with self polysialic acid (PSA) antigenspresent on human tissues. The minimal deNAc SA epitope is a disaccharideof sialic acid residues in which one or both residues containde-N-acetyl residues. The minimal deNAc SA epitope can also be describedas a disaccharide unit comprising one or more sialic acid residues inwhich the N-acetyl group on the C-5 amino group has been removed leavinga free amine or, where one of the two residues are de-N-acetylated, thesecond residue contains an N-acetyl group (but, in some embodiments, notan N-propionyl group). The disaccharide unit defining this minimalepitope may be at the reducing end, the non-reducing end, or within apolymer of sialic acid residues (e.g., within a polysaccharide).De-N-acetylated residues in the context of PSA containing N-acylatedresidues are immunogenic and elicit antibodies that are reactive withthe deNAc SA epitiope, but are minimally reactive or not detectablyreactive with human PSA antigens.

The de-N-acetylated NmB polysaccharide epitope was identified using amurine anti-N—Pr NmB polysaccharide mAb (monoclonal antibodies), SEAM 3,described in Granoff et al., 1998, J Immunol 160:5028 (anti-N—Pr NmB PSmAbs); U.S. Pat. No. 6,048,527 (anti-NmB antibodies); and U.S. Pat. No.6,350,449 (anti-NmB antibodies).

The invention features deNAc SA epitopes, and formulations of suchadapted for administration to a host to elicit an anti-deNAc SA epitopeantibody response. The deNAc SA antigen compositions can be adapted foradministration to a subject to elicit an anti-deNAc SA epitope immuneresponse, particularly an anti-deNAc SA epitope antibody response, whichimmune response is directed against deNAc SA epitopes on a surface ofcertain cancerous cells, as discussed in detail below. The deNAc SAantigen compositions can also be used to generate antibodies thatspecifically bind a deNAc SA epitope on a surface of a cancerous cell(e.g., a deNAc ganglioside or deNAc sialic acid-modified surfaceaccessible protein). Such antibodies are useful in antibody-based cancertherapy.

Other features of the invention are described herein, and will also bereadily apparent to the ordinarily skilled artisan upon reading thepresent disclosure.

Definitions

Definitions provided herein shall control relative to those set out inthe priority application.

The term “de-N-acetyl sialic acid antigen” (which may also be referredto as “de-N-acetylated sialic acid antigen” or “deNAc SA antigen”)refers to a compound having or mimicking a deNAc sialic acid epitope(deNAc SA epitope), which epitope is minimally defined by a dimer ofresidues of sialic acid or sialic acid derivative, where the dimercontains at least one de-N-acetylated sialic acid residue adjacent anN-acylated (e.g., acetylated or propionylated) sialic acid residue or asialic acid derivative residue. Examples of de-N-acetyl sialic acidantigens are provided in the present disclosure, and include, withoutlimitation, de-N-acetylated polysaccharide derivatives (“PSderivatives”), de-N-acetylated gangliosides, and de-N-acetylatedderivatives of a sialic-acid modified protein, particularly asialic-acid modified protein that is accessible at an extracellularsurface of a mammalian cell, particularly a human cell, moreparticularly a cancer cell, particularly a human cancer cell. It shouldbe noted that description of a deNAc SA antigen as a derivative of astarting molecule (e.g., PS derivative or ganglioside derivative) is notmeant to be limiting as to the method of production of the de-N-acetylsialic acid antigen, but rather is meant as a convenient way to describethe structure of the exemplary deNAc SA antigen.

“SEAM 3-reactive antigen” refers to an antigen having an epitope that isspecifically bound by the monoclonal antibody (mAb) SEAM 3 (ATCC DepositNo. HB-12170). Exemplary SEAM 3-reactive antigens are provided in theworking examples.

“Cell surface antigen” (or “cell surface epitope”) refers to an antigen(or epitope) on surface of a cell that is extracellularly accessible atany cell cycle stage of the cell, including antigens that arepredominantly or only extracellularlly accessible during cell division.“Extracellularly accessible” in this context refers to an antigen thatcan be bound by an antibody provided outside the cell without need forpermeabilization of the cell membrane.

“PS” as used herein refers to polysaccharide, usually a capsularpolysaccharide, particularly a capsular polysaccharide having one ormore de-N-acetylated residues, including capsular polysaccharide of N.meningitidis or Escherichia coli, with N. meningitidis Group B and E.coli K1 being of particular interest. “NmB PS” as used herein refers toa PS of a Group B N. meningitidis. Reference to NmB PS throughout thespecification is meant to be exemplary of PS structures amenable forproduction of compositions and use in methods of the invention.

“PS derivative” as used herein refers to a modified, usually chemicallymodified, polysaccharide (PS), particularly a PS of Neisseriameningitidis Group B (NmB) or Escherichia coli K1, with PS derivativeshaving a free amine (i.e., a primary amine) in lieu of one or moreN-acetyl groups being of particular interest. In some embodiments, PSderivatives are NmB. In other other embodiments, the PS derivatives arebiosynthetically produced ganglioside derivatives (e.g., produced in amammalian cell, e.g., a cancerous mammalian cell). “PS derivative” asused herein includes protected PS derivativies, such as those describedherein.

“de-N-acetylated PS derivative” as used herein refers to a PS derivativehaving one or more de-N-acetylated residues, e.g., one or more freeamines at the C-5 position of one or more residues of the polysaccharidederivative. The term “de-N-acetylated PS derivative” is not meant toimply that de-N-acetylated PS derivatives are limited to PS derivativesgenerated by a process involving removing an acetyl group from a PSmolecule, but instead, unless specifically indicated otherwise, is meantto encompass de-N-acetylated PS derivatives generated by any suitablemethod (e.g., by a biosynthetic method in which free amines aregenerated in a de-N-acetylated PS derivative by removal of a trihaloacylprotecting group incorporated into the PS molecule during PSbiosynthesis). Further, “de-N-acetylated residue” is used herein in thecontext of a PS derivative to refer to a sialic acid residue in themolecule that has, in lieu of a native acetyl group, a primary amine

“Free amine” and “primary amine” are used interchangeably herein torefer to an NH2 group, as in, for example, RNH₂ where “R” is a sialicacid residue of a PS derivative of the invention.

“deNAc SA antigen conjugate” refers to a deNAc SA antigen linked,usually covalently linked, to a carrier molecule (such as a carrierprotein). Exemplary de-N-acetyl sialic acid antigen conjugates include a“PS conjugate”, which generally refers to a conjugate of a carriermolecular (such as a carrier protein) and a homolinear polymer ofalpha(2→8) N-acetyl neuraminic acid or any other polysaccharidecontaining this monomeric unit, or derivatives thereof, includingde-N-acetylated PS derivatives of the invention. Of particular interestis a conjugate of a carrier protein and a derivative of Neisseriameningitidis capsular polysaccharide (particularly a Group B capsularpolysaccharide), particularly a de-N-acetylated PS derivative of theinvention. Also of particular interest is a conjugate of a carrierprotein and a derivative of E. coli K1 capsular polysaccharide,particularly a de-N-acetylated PS derivative of the invention.

“Carrier” as used in the context of a carrier conjugated to ade-N-acetyl sialic acid antigen generally refers to a substance that,when linked to an antigen, serves as a T-dependent antigen which canactivate and recruit T-cells and thereby augment T-cell dependentantibody production. The carrier need not be strongly immunogenic byitself, although strongly immunogenic carriers are within the scope ofthis invention. Carriers in this context are generally polypeptides,which can be all or a fragment of a protein.

“Conjugated” generally refers to a chemical linkage, either covalent ornon-covalent, usually covalent, that proximally associates thede-N-acetylated PS with the carrier so that the carrier-conjugatedde-N-acetyl sialic acid antigen has increased immunogenicity relative tounconjugated de-N-acetyl sialic acid antigen.

“Chemotherapy” as used herein refers to use of an agent (e.g., drug,antibody, etc.), particularly an agent(s) that is selectivelydestructive to a cancerous cell, in treatment of a disease, withtreatment of cancer being of particular interest.

“Immunotherapy” refers to treatment of disease (e.g., cancer) bymodulating an immune response to a disease antigen. In the context ofthe present application, immunotherapy refers to providing ananti-cancer immune response in a subject by administration of anantibody (e.g., a monoclonal antibody) and/or by administration of anantigen the elicits an anti-tumor antigen immune response in thesubject.

“Treatment” or “treating” as used herein means any therapeuticintervention in a subject, usually a mammalian subject, generally ahuman subject, including: (i) prevention, that is, reducing the risk ofdevelopment of clinical symptoms, including causing the clinicalsymptoms not to develop, e.g., preventing disease progression to aharmful state; (ii) inhibition, that is, arresting the development orfurther development of clinical symptoms, e.g., mitigating or completelyinhibiting an active disease, e.g., so as to decrease tumor load, whichdecrease can include elimination of detectable cancerous cells; and/or(iii) relief, that is, causing the regression of clinical symptoms.

The term “protective immunity” means that a vaccine or immunizationschedule that is administered to a mammal induces an immune responsethat prevents, retards the development of, or reduces the severity of adisease (e.g., cancer), or diminishes or altogether eliminates thesymptoms of the disease.

By “autoreactive” in the context of antibody binding is meant that theantibody exhibits significant binding to a host antigen (e.g.,polysialic acid (PSA) native to a host). Autoreactive antibodies includethose that bind to host antigens (e.g., PSA on non-cancerous host cells)as well as to foreign antigens (e.g., to a tumor antigen presented by acancerous cell, to NmB PS or E. coli K1 PS). A “non-autoreactiveantibody” is an antibody that does not significantly or detectably bindto a host antigen, with not detectable binding to a native host antigenbeing of particular interest. Non-autoreactive antibodies of interestare antibodies that specifically bind a de-N-acetyl sialic acid epitope(e.g., a deNAc SA epitope of a de-N-acetylated ganglioside of a cancercell, a deNAc SA epitope of NmB PS or E. coli K1 PS), which antibodiescan facilitate reduction of viability to a cell to which the antibodybinds (e.g., are, bactericidal for NmB and/or E. coli K1 and/orfacilitate reduction of cell viability of a cancer cell).

The phrase “in a sufficient amount to elicit an immune response” (e.g.,to epitopes present in a preparation) means that there is a detectabledifference between an immune response indicator measured before andafter administration of a particular antigen preparation. Immuneresponse indicators include but are not limited to: antibody titer orspecificity, as detected by an assay such as enzyme-linked immunoassay(ELISA), flow cytometry, immunoprecipitation, Ouchter-Lowryimmunodiffusion; binding detection assays of, for example, spot, Westernblot or antigen arrays; cytotoxicity assays, and the like.

The term “antibody” (also used interchangeably with “immunoglobulin”)encompasses polyclonal and monoclonal antibody preparations where theantibody may be of any class of interest (e.g., IgM, IgG, and subclassesthereof), as well as preparations including hybrid antibodies, alteredantibodies, F(ab′)₂ fragments, F(ab) molecules, Fv fragments, singlechain fragment variable displayed on phage (scFv), single chainantibodies, single domain antibodies, chimeric antibodies, humanizedantibodies, and functional fragments thereof which exhibit immunologicalbinding properties of the parent antibody molecule. In some embodiments,e.g., cancer therapy, antibodies that provide for complement-mediatedkilling and/or antibody-dependent cellular cytotoxicity (ADCC) are ofparticular interest. The antibodies described herein may be detectablylabeled, e.g., with a radioisotope, an enzyme which generates adetectable product, a fluorescent protein, and the like. The antibodiesmay be further conjugated to other moieties, such as a cytotoxicmolecule or other molecule (e.g., to provide for delivery of ananti-cancer drug to a cancer cell), members of specific binding pairs,e.g., biotin (member of biotin-avidin specific binding pair), and thelike. The antibodies may also be bound to a support (e.g., a solidsupport), such as a polystyrene plate or bead, test strip, and the like.

Immunoglobulin polypeptides include the kappa and lambda light chainsand the alpha, gamma (IgG₁, IgG₂, IgG₃, IgG₄), delta, epsilon and muheavy chains or equivalents in other species. Full-length immunoglobulin“light chains” (usually of about 25 kDa or about 214 amino acids)comprise a variable region of about 110 amino acids at the NH₂-terminusand a kappa or lambda constant region at the COOH-terminus. Full-lengthimmunoglobulin “heavy chains” (of about 50 kDa or about 446 aminoacids), similarly comprise a variable region (of about 116 amino acids)and one of the aforementioned heavy chain constant regions, e.g., gamma(of about 330 amino acids).

An immunoglobulin light or heavy chain variable region is composed of a“framework” region (FR) interrupted by three hypervariable regions, alsocalled “complementarity determining regions” or “CDRs”. The extent ofthe framework region and CDRs have been precisely defined (see,“Sequences of Proteins of Immunological Interest,” E. Kabat et al., U.S.Department of Health and Human Services, (1991 and Lefranc et al. IMGT,the international ImMunoGeneTics information system®. Nucl. Acids Res.,2005, 33, D593-D597)). A detailed discussion of the IMGTS system,including how the IMGTS system was formulated and how it compares toother systems, is provided on the World Wide Web at imgt.cines.fr/textes/ IMGTScientificChart/ Numbering/ IMGTnumberingsTable.html. Thesequences of the framework regions of different light or heavy chainsare relatively conserved within a species. The framework region of anantibody, that is the combined framework regions of the constituentlight and heavy chains, serves to position and align the CDRs. The CDRsare primarily responsible for binding to an epitope of an antigen.

“Chimeric antibodies” refers to antibodies having light and/or heavychain genes that have been constructed, typically by geneticengineering, from antibody variable and constant region genes belongingto different antibodies, e.g., of a different species. For example, thevariable segments of the genes from a non-human (e.g., mouse) monoclonalantibody may be joined to human constant segments, such as gamma 1 andgamma 3. An example of a therapeutic chimeric antibody is a hybridprotein composed of the variable or antigen-binding domain from anon-human (e.g., mouse) antibody and the constant or effector domainfrom a human antibody, although other mammalian species may be used.

As used herein, the term “humanized antibody” or “humanizedimmunoglobulin” refers to an non-human (e.g., mouse or rabbit) antibodycontaining one or more amino acids (in a framework region, a constantregion or a CDR, for example) that have been substituted with acorrespondingly positioned amino acid from a human antibody. In general,humanized antibodies produce a reduced immune response in a human host,as compared to a non-humanized version of the same antibody.

It is understood that the humanized antibodies designed and produced bythe present method may have additional conservative amino acidsubstitutions which have substantially no effect on antigen binding orother antibody functions. By conservative substitutions is intendedcombinations such as those from the following groups: gly, ala; val,ile, leu; asp, glu; asn, gln; ser, thr; lys, arg; and phe, tyr.

A “variant” of a polypeptide, such as a variant antibody, is defined asa polypeptide that is altered by one or more amino acid residuesrelative to a reference sequence, e.g., a parent polypeptide, which maybe a naturally occurring polypeptide. Such alterations include aminoacid substitutions, deletions or insertions, or a combination thereof.Variants of an antibody heavy chain or light chain polypeptide ofinterest are those retain their basic structural features and biologicalactivity in binding to an antigen of interest and, in some embodimens,biological activity in effecting reduction of viability of a cancercell.

Guidance in determining which and how many amino acid residues may besubstituted, inserted or deleted may be found by comparing the sequenceof a polypeptide to the sequence of a polypeptide with a relatedstructure and function e.g., sequences from other sources (e.g.,comparison between sequences from mammalian sources, e.g., human, rat,mouse, and the like).

The term “specific binding of an antibody” or “antigen-specificantibody” in the context of a characteristics of an antibody refers tothe ability of an antibody to preferentially bind to a particularantigen that is present in a homogeneous mixture of different antigens.In certain embodiments, a specific binding interaction will discriminatebetween desirable and undesirable antigens (or “target” and “non-target”antigens) in a sample, in some embodiments more than about 10 to100-fold or more (e.g., more than about 1000- or 10,000-fold). Incertain embodiments, the affinity between an antibody and antigen whenthey are specifically bound in an antibody-antigen complex ischaracterized by a K_(D) (dissociation constant) of less than 10⁻⁶ M,less than 10⁻⁷ M, less than 10⁻⁸ M, less than 10⁻⁹ M, less than 10⁻⁹ M,less than 10⁻¹¹ M, or less than about 10⁻¹² M or less.

The phrase “specifically binds to an antibody” or “specificallyimmunoreactive with” is also used when referring to an antigen such as apolysaccharide, phospholipid, protein or peptide, especially in thecontext of a binding reaction which is based on and/or is probative ofthe presence of the antigen under conditions which may also include aheterogeneous population of other molecules (e.g., as in a sample or invivo). Thus, under the relevant conditions (e.g., designated immunoassayconditions), the specified antibody or antibodies bind(s) to aparticular antigen or antigens and does not bind in a significant amountto other molecules present in the sample, particularly when compared tobinding to an epitope of a target antigen against which the antibody wasraised.

A “substitution” results from the replacement of one or more amino acidsor nucleotides by different amino acids or nucleotides, respectively ascompared to an amino acid sequence or polypeptide or nucleic acid. Inthe context of polypeptides, if a substitution is conservative, theamino acid that is substituted into a polypeptide has similar structuralor chemical properties (e.g., charge, polarity, hydrophobicity, and thelike) to the amino acid that it is substituting. Conservativesubstitutions of naturally occurring amino acids usually result in asubstitution of a first amino acid with second amino acid from the samegroup as the first amino acid, where exemplary amino acid groups are asfollows: gly, ala; val, ile, leu; asp, glu; asn, gln; ser, thr; lys,arg; and phe, tyr.

A “deletion” is defined as a change in either amino acid or nucleotidesequence in which one or more amino acid or nucleotide residues,respectively, are absent as compared to an amino acid sequence ornucleotide sequence of a naturally occurring polypeptide. In the contextof a polypeptide and polypeptide element amino acid or polynucleotidesequence, a deletion can involve deletion of about 2, about 5, about 10,up to about 20, up to about 30 or up to about 50 or more amino acids. Apolypeptide according to the invention may contain more than onedeletion.

An “insertion” or “addition” is that change in an amino acid ornucleotide sequence which has resulted in the addition of one or moreamino acid or nucleotide residues, respectively, as compared to an aminoacid sequence or nucleotide sequence of a naturally occurringpolypeptide. “Insertion” generally refers to addition to one or moreresidues within a sequence of a polypeptide or nucleic acid, while“addition” can be an insertion or refer to amino acid residues added atthe N- or C-termini of a polypeptide or to nucleotides added to the 5′or 3′ ends of a nucleic acid. An insertion or addition may be of up toabout 10, up to about 20, up to about 30 or up to about 50 or more aminoacids.

“Corresponding amino acids”, as will be exemplified below, are aminoacid residues that are at an identical position (i.e., they lie acrossfrom each other) when two or more amino acid sequences are aligned.Methods for aligning and numbering antibody sequences are set forth ingreat detail in Chothia, supra, Kabat supra, and others. As is known inthe art (see, e.g. Kabat 1991 Sequences of Proteins of ImmunologicalInterest, DHHS, Washington, DC), sometimes one, two or three gaps and/orinsertions of up to one, two, three or four residues, or up to about 15residues (particularly in the L3 and H3 CDRs) may be made to one or bothof the amino acids of an antibody in order to accomplish an alignment.

A “natural” antibody is an antibody in which the heavy and lightimmunoglobulins of the antibody have been naturally selected by theimmune system of a multi-cellular organism, as opposed to unnaturallypaired antibodies made by e.g. phage display, or humanized antibodies.As such, the subject parental antibodies do not usually contain anyviral (e.g., bacteriophage M13)-derived sequences. Spleen, lymph nodesand bone marrow are examples of tissues that produce natural antibodies.

A “substitutable position”, as in the context of variants of a givenantibody heavy chain or light chain polypeptide, is a particularposition of a polypeptide amino acid sequence that may be substituted bydifferent amino acids, preferably without significantly decreasing thebinding activity of the antibody. Methods for identifying substitutablepositions, and how they may be substituted, are described in muchgreater detail below. A substitutable positions may also be referred toas “variation tolerant position”.

A “parent” antibody, as will be described in greater detail below, is anantibody that is the template or target for amino acid modifications. Incertain embodiments, amino acids may be “donated” by a “donor” antibodyto the parent antibody to produce an altered antibody.

“Related antibodies”, as will be described in greater detail below, areantibodies that have a similar sequence and produced by cells that havea common B cell ancestor. Such a B cell ancestor contains a genomehaving a rearranged light chain VJC region and a rearranged heavy chainVDJC region, and produces an antibody that has not yet undergoneaffinity maturation. “Naïve” or “virgin” B cells present in spleentissue, are exemplary B cell common ancestors. Related antibodies bindto the same epitope of an antigen and are typically very similar insequence, particularly in their L3 and H3 CDRs. Both the H3 and L3 CDRsof related antibodies have an identical length and a near identicalsequence (i.e., differ by 0, 1 or 2 residues). Related antibodies arerelated via a common antibody ancestor, the antibody produced in thenaïve B cell ancestor. The term “related antibodies” is not intended todescribe a group of antibodies that do not have a common antibodyancestor produced by a B-cell.

A “variable region” of a heavy or light antibody chain is an N-terminalmature domain of the chains. V_(H) is the variable domain of an antibodyheavy chain. V_(L) is the variable domain of an antibody light chain,which could be of the kappa (K) or of the lambda isotype. K-1 antibodieshave the kappa-1 isotype whereas K-2 antibodies have the kappa-2 isotypeand V_(L) is the variable lambda light chain.

As used herein, the term “monoclonal antibody” refers to an antibodycomposition having a homogeneous antibody population. The term is notlimited by the manner in which it is made. The term encompasses wholeimmunoglobulin molecules, as well as Fab molecules, F(ab′)₂ fragments,Fv fragments, single chain fragment variable displayed on phage (scFv),fusion proteins comprising an antigen-binding portion of an antibody anda non-antibody protein, and other molecules that exhibit immunologicalbinding properties of the parent monoclonal antibody molecule. Methodsof making polyclonal and monoclonal antibodies are known in the art anddescribed more fully below.

The terms “polypeptide” and “protein”, used interchangeably herein,refer to a polymeric form of amino acids of any length, which caninclude coded and non-coded amino acids, chemically or biochemicallymodified or derivatized amino acids, and polypeptides having modifiedpeptide backbones. The term includes fusion proteins, including, but notlimited to, fusion proteins with a heterologous amino acid sequence,fusions with heterologous and homologous leader sequences, with orwithout N-terminal methionine residues; immunologically tagged proteins;fusion proteins with detectable fusion partners, e.g., fusion proteinsincluding as a fusion partner a fluorescent protein, β-galactosidase,luciferase, etc.; and the like. Polypeptides may be of any size, and theterm “peptide” refers to polypeptides that are 8-50 residues (e.g., 8-20residues) in length.

“Heterologous” as used in the context of a nucleic acid or polypeptidegenerally means that the nucleic acid or polypeptide is from a differentorigin (e.g., molecule of different sequence, different species origin,and the like) than that with which the nucleic acid or polypeptide isassociated or joined, such that the nucleic acid or polypeptide is onethat is not found in nature. For example, in a fusion protein, a lightchain polypeptide and a reporter polypeptide (e.g., GFP) are said to be“heterologous” to one another. Similarly, a CDR from a mouse antibodyand a constant region from a human antibody are said to be“heterologous” to one another.

By “isolated” is meant that a compound is separated from all or some ofthe components that accompany it in nature. “Isolated” also refers tothe state of a compound separated from all or some of the componentsthat accompany it during manufacture (e.g., chemical synthesis,recombinant expression, culture medium, and the like).

By “purified” is meant a compound of interest has been separated fromcomponents that accompany it in nature and provided in an enriched form.“Purified” also refers to a compound of interest separated fromcomponents that can accompany it during manufacture (e.g., in chemicalsynthesis, recombinant expression, culture medium, and the like) andprovided in an enriched form. Typically, a compound is substantiallypure when it is at least 50% to 60%, by weight, free from organicmolecules with which it is naturally associated or with which it isassociated during manufacture. Generally, the preparation is at least75%, more usually at least 90%, and generally at least 99%, by weight,of the compound of interest. A substantially pure compound can beobtained, for example, by extraction from a natural source (e.g.,bacteria), by chemically synthesizing a compound, or by a combination ofpurification and chemical modification. A substantially pure compoundcan also be obtained by, for example, enriching a sample having acompound that binds an antibody of interest. Purity can be measured byany appropriate method, e.g., chromatography, mass spectroscopy, HPLCanalysis, etc.

“Enriched” means that a substance (e.g., antibody or antigen) in acomposition is manipulated by an experimentalist or a clinician so thatit is present in at least a two-fold greater concentration by weight,usually at least three-fold greater concentration by total weight,usually at least 10-fold greater concentration, more usually at least100-fold greater concentration, and still more usually at least1,000-fold greater concentration than the concentration of that antigenin the strain from which the antigen composition was obtained. Thus, forexample, if the concentration of a particular antigen is 1 microgram pergram of total preparation (or of total protein), an enriched preparationwould contain at least 3 micrograms per gram of total preparation (or oftotal protein).

“Inactivation” of a cell is used herein to indicate that the cell hasbeen rendered incapable of cell division to form progeny. The cell maynonetheless be capable of response to stimulus and/or biosynthesis for aperiod of time, e.g., to provide for production of a cell surfacemolecule (e.g., cell surface protein or polysaccharide).

The term “immunologically naïve with respect to a deNAc SA antigen”denotes an individual (e.g., a mammal such as a human patient) that hasnot been exposed to de-N-acetyl sialic acid antigen described herein(e.g., a PS derivative), either alone or in the context of a largermolecule, in sufficient amounts to cause an immune response (e.g., toprime). If the individual has been exposed to a de-N-acetyl sialic acidantigen conjugate vaccine (in one or more doses), the individual has apropensity for production of antibodies.

A “primed” subject refers to a subject that has been exposed (e.g., byadministration) to an antigen (e.g., a de-N-acetylated SA antigen) in asufficient amount to elicit an immune response that, upon subsequentexposure to the same or second antigen (e.g., a de-N-acetyl sialic acidantigen conjugate), provides for a protective immune response.

By “no clinically relevant autoantibody response” is meant thatproduction of autoantibodies is reduced by at least 25%, at least 40%,at least 50%, at least 60%, at least 75%, at least 80% or more using theimmunization methods disclosed herein compared to autoantibodyproduction following immunization of naïve subject with a conventionalNmB polysaccharide vaccine (e.g., a PS conjugate vaccine as described inU.S. Pat. No. 4,727,136 (N—Pr-NmB conjugate vaccine)).

“Pharmaceutically acceptable excipient” as used herein refers to anysuitable substance which provides a pharmaceutically acceptable vehiclefor administration of a compound(s) of interest to a subject.“Pharmaceutically acceptable excipient” can encompass substancesreferred to as pharmaceutically acceptable diluents, pharmaceuticallyacceptable additives and pharmaceutically acceptable carriers.

“In combination with” as used herein refers to uses where, for example,a first therapy is administered during the entire course ofadministration of a second therapy; where the first therapy isadministered for a period of time that is overlapping with theadministration of the second therapy, e.g. where administration of thefirst therapy begins before the administration of the second therapy andthe administration of the first therapy ends before the administrationof the second therapy ends; where the administration of the secondtherapy begins before the administration of the first therapy and theadministration of the second therapy ends before the administration ofthe first therapy ends; where the administration of the first therapybegins before administration of the second therapy begins and theadministration of the second therapy ends before the administration ofthe first therapy ends; where the administration of the second therapybegins before administration of the first therapy begins and theadministration of the first therapy ends before the administration ofthe second therapy ends. As such, “in combination” can also refer toregimen involving administration of two or more therapies. “Incombination with” as used herein also refers to administration of two ormore therapies which may be administered in the same or differentformulations, by the same of different routes, and in the same ordifferent dosage form type.

The terms “subject,” “host,” “patient,” and “individual” are usedinterchangeably herein to refer to any mammalian subject for whomdiagnosis or therapy is desired, particularly humans Other subjects mayinclude cattle, dogs, cats, guinea pigs, rabbits, rats, mice, horses,and so on.

In the context of cancer therapies and diagnostics described herein,“subject” or “patient” is used interchangeably herein to refer to asubject having, suspected of having, or at risk of developing a tumor,where the cancer is one associated with cancerous cells having ade-N-acetyl sialic acid antigen at a cell surface (e.g., an at leastpartially de-N-acetylated ganglioside, de-N-acetylated sialicacid-modified protein). Samples obtained from such subject are likewisesuitable for use in the methods of the invention.

As used herein, the terms “determining,” “measuring,” and “assessing,”and “assaying” are used interchangeably and include both quantitativeand qualitative determinations.

It is further noted that the claims may be drafted to exclude anyoptional or alternative element. As such, this statement is intended toserve as antecedent basis for use of such exclusive terminology as“solely”, “only” and the like in connection with the recitation of claimelements, or the use of a “negative” limitation.

DENAc SA Antigens and Conjugates

De-N-acetyl sialic acid (deNAc SA) antigens of the present disclosurecontain at least a minimal epitope of a dimer of residues of sialic acidor sialic acid derivative, where the dimer contains at least onede-N-acetyl sialic acid residue adjacent an N-acylated (e.g., acetylatedor propionylated) sialic acid residue or a sialic acid derivativeresidue. This dimeric epitope, referred to herein as a deNAc SA epitope,can be positioned within any solvent accessible region of a de-N-acetylsialic acid antigen. For example, where the deNAc SA antigen ispositioned within a polymer (e.g., a polysaccharide), e.g., as in ade-N-acetylated PS derivative, the deNAc SA epitope can be positioned atthe reducing end, the non-reducing end, or within the interior of thecompound (e.g., 1, 2, 3, 4, 5, 10 or more residues from the reducing endor non-reducing end of the compound). The dimeric epitope can be presentas one or more dimeric units within a deNAc SA antigen (e.g., asconsecutive or nonconsecutive dimeric repeating units), or can bepresent within other units present in the deNAc SA, e.g., within atrimeric unit, which may be present as consecutive or nonconsecutiverepeating units). Exemplary molecules within the scope of the inventionare set out in FIGS. 6-33.

It should be noted that all deNAc SA compounds described herein,including those having a bacterial PS or a ganglioside as a startingmaterial or backbone, can be used in any of the immunization,therapeutic, and diagnostic methods described herein. Thus, for example,a deNAc SA antigen (e.g., generated using a NmB PS) can be used in thecontext of a cancer vaccine and used to raise antibodies that can beused in treatment or cancer. Likewise, a de-N-acetyl sialic acid antigen(e.g., such as one generated using a mammalian cell ganglioside) can beused in the context of a NmB vaccine and to detect NmB in a diagnostic.

deNAc SA antigens described herein, and useful in the methods of theinvention, generally comprise at least one dimeric epitope, which can bepresent in a completely de-N-acetylated polysaccharide or an at leastpartially de-N-acetylated polysaccharide, and can be present in ahomopolymeric or heteropolymeric molecule. For example, a deNAc SAantigen can comprise one or more structures as set out below (see, e.g.,Formulae I-VIII below). deNAc SA antigens can comprise 2, 3, 4, 5, 6, 7,8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50,55, 60 or more sialic acid residues or derivatives thereof, and may havea degree of polymerization (Dp) of about 2 to about 60, about 10 toabout 50, about 30 to about 50, about 10 to 20, or about 12 to about 18,with a Dp of about 2 to about 10 being of particular interest. deNAc SAantigens that are smaller in size can comprise further modifications(e.g., be conjugated to a carrier, lipidated, and the like) to providemolecules of suitable size and/or immunogenicity. DeNAc SA antigens canadditionally comprise 3, 4, 5, 6, 7, 8, 9 or 10 or more adjacentde-N-acetylated residues, wherein in some embodiments, particularlywhere the deNAc SA antigen is composed of only N-acetylated andde-N-acetylated residues and is not further modified (e.g., byconjugation to a carrier or by modification of a sialic acid residue atthe reducing end to contain a secondary alkyl amine), thede-N-acetylated residues of a deNAc SA antigen may be 30% or less of thetotal sialic acid residues of the molecule, and N-acetylated residuesmay be about 70% or more of the total sialic acid residues of themolecule. It should be noted that “de-N-acetylated” refers to any numberof de-N-acetyl sialic acid residues in a polymer of sialic acidresidues, provided the minimal deNAc SA epitope is present, and thus“de-N-acetylated” encompasses the term “at least partiallyde-N-acetylated”.

DeNAc SA antigens of particular interest are those that, whenadministered to a subject elicit production of antibodies that bind acancer cell that exhibits a deNAc SA epitope, are not significantly ordetectably cross-reactive with PSA of the subject (e.g., human PSA foundon non-cancerous cells). Anti-deNAc SA antigen antibodies are those thatfacilitate reduction of viability of a deNAc SA epitope-presentingcancer cell.

In general, deNAc SA antigens of interest are at least partiallyde-N-acylated, so that the deNAc SA antigens are zwitterionic compoundscomposed of, for example, polysaccharide residues or derivativesthereof, and comprise one or more dimers, and/or one or more trimers,which comprise an epitope as described above. The deNAc SA antigens,such as de-N-acetyl PS derivatives in general comprise at least onedimeric epitope, where the dimeric epitope is characterized by having(1) first and second de-N-acetylated residues; (2) a first N-acylatedresidue and a second adjacent de-N-acylated residue (i.e., a residuehaving a free amine group), where the N-acylated residue is not anN-propionyl (N—Pr) group; or (3) a first de-N-acylated residue (i.e., aresidue having a free amine group) and a second adjacent N-acylatedresidue. In certain embodiments, the N-acylated residue comprises anunsaturated acyl group; in further embodiments, the N-acylated residuedoes not comprise an N-propionyl (N—Pr) group (i.e., the sialic acidresidue in the dimer is not N-propionylated).

As used herein an “acyl group” includes a saturated or unsaturated acylgroup, usually a saturated or unsaturated C₂₋₁₈ acyl group, a saturatedor unsaturated C₂₋₁₆ acyl group, a saturated or unsaturated C₂₋₁₂ acylgroup, a saturated or unsaturated C₂₋₁₀ acyl group, a saturated orunsaturated C₂₋₈ acyl group, a saturated or unsaturated C₂₋₆ acyl group,a saturated or unsaturated C₂₋₄ acyl group, or a saturated C₂₋₄ acylgroup. A saturated acyl group as used herein is intended to refer to acarbonyl joined to a saturated alkyl group; an unsaturated acyl group asused herein is intended to refer to a carbonyl joined to an unsaturatedalkyl group. In some embodiments, unsaturated acyl groups are ofparticular interest. The residues of the dimer can be a sialic acid orsialic acid derivative, such as a lactone or cyclic sialic acid.

Accordingly, the deNAc SA antigens comprise one or more de-N-acetylatedresidues of a sialic acid moiety or derivative thereof (e.g., a lactone,cyclic sialic acid, and the like), which de-N-acetylated residues can bepositioned within the deNAc SA antigen at the reducing end, thenon-reducing end, or within the interior of a polymer of sialic acidresidues (i.e., between the reducing and non-reducing ends), with deNAcSA antigens having de-N-acetylated residues at the reducing end of thepolysaccharide polymer being of particular interest.

The deNAc SA antigens may be provided as a structure comprising a singledimeric epitope, or a polymeric unit comprising two or more dimericepitopes. DeNAc SA antigens may be homopolymeric or heteropolymericstructures, which can be composed of one or more of the structures belowas well as, in some embodiments, additional de-N-acetylated orN-acetylated sialic acid residues. Where a formula is provided belowwith reference to “n” units (e.g., units of a dimeric or trimericstructure), the deNAc SA antigen can comprise multiple of such “n”units. For example, a deNAc SA antigen can comprise 2, 3, 4, 5, 6, 7, 8,9 10 or more consecutive or non-consecutive units of a given dimeric ortrimeric structure, where “n” refers to the number of consecutivedimeric or trimeric structures within each unit. Such dimeric andtrimeric units can be separated by sialic residues.

The deNAc SA antigens can further comprise additional moieties attachedto a sialic acid residue or derivative thereof at the non reducingterminus, reducing-terminus or both the non-reducing- andreducing-termini of the polysaccharide polymer.

In one embodiment, deNAc SA antigens include those comprising astructure represented by the formula:

wherein

X and Y are independently H, an amine protecting group (e.g., atrihaloacyl group), or a saturated or unsaturated acyl group (usually asaturated acyl group), where in some embodiments, X and Y areindependently 1) H or an amine protecting group; or 2) a saturated orunsaturated acyl group, and

n is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more, usually 5 orgreater, more usually about 10 or greater, and may have a degree ofpolymerization (Dp) of about 2 to about 60, about 10 to about 50, about30 to about 50, about 10 to 20, or about 12 to about 18, with a Dp ofabout 2 to about 10 being of particular interest,

and further wherein

when X is a saturated or unsaturated acyl group (in some embodiments,other than a propionyl group and, in further embodiments, other than anunsaturated acyl group), Y is H or an amine protecting group; and

when Y is a saturated or unsaturated acyl group (in some embodiments,other than a propionyl group and, in further embodiments, other than anunsaturated acyl group); X is H an amine protecting group. In anotherembodiment of particular interest, X and Y are independently H or asaturated or unsaturated acyl group, usually an unsaturated acyl group,In further embodiments, X and Y are independently an amine protectinggroup (e.g., a trihaloacyl group) or a saturated or unsaturated acylgroup, usually a saturated acyl group. In some embodiments, particularlywhere X or Y is H or an unsaturated acyl group, the PS derivative isless than 90%, usually less than 85%, or less than 80% N-acylated,particularly where the PS derivative comprises at least 10 or 20residues.

In an embodiment of interest, X in Formula I is a saturated acyl groupand Y is H or an amine protecting group. In an embodiment of particularinterest, X in Formula I is an acetyl group and Y is H or an amineprotecting group (e.g., a trihaloacyl group (e.g., a trihaloacetylgroup)). In another embodiment of interest, X in Formula I is asaturated acyl group and Y is H; or X is an acetyl group and Y is H.

Where either X or Y are an amine protecting group (e.g., a trihaloacylgroup), such deNAc SA antigens are referred to herein as “protecteddeNAc SA antigens” (e.g,. “protected PS derivatives”), where the amineprotecting group acts to prevent the amine group from undergoing areaction during further modification of the protected deNAc SA antigen,e.g., conjugation of the molecule to a carrier (e.g.,. a carrierprotein), addition of a lipid moiety (e.g., addition of an acyl amine ata non-reducing end of a protected PS derivative), and the like. Theamine protecting group can subsequently be modified to provide a freeamine at the residue. Protected deNAc SA antigens in general areexemplified by the structures described herein, where an amineprotecting group is present at a variable position in lieu of ahydrogen. That is, where a hydrogen might be desired in a deNAc SAantigen to provide a free amine, protected DeNAc SA antigens contain anamine protecting group at that residue in lieu of the hydrogen of thefree amine

As used herein “amine protecting group” refers to a radical or group ofatoms that is bound to an amine nitrogen atom of a molecule to preventthat nitrogen atom from participating in reactions occurring on otherportions of the molecule. The term “amine-protected” denotes thestructural characteristic of a molecule containing an amine nitrogenatom by which that nitrogen atom is prevented from participating inreactions occurring on other portions of the molecule.

Exemplary amine protecting groups for use in the invention include, butare not necessarily limited to, carbamates, amides, N-alkyl and N-arylamines, imine derivatives, enamine derivatives, N-sulfonyls, and thelike. Further exemplary amine protecting groups include, but are notnecessarily limited to: acyl types such as formyl, trifluoroacetyl,phthalyl, and p-toluenesulfonyl; aromatic carbamate types such asbenzyloxycarbonyl (Cbz) and substituted benzyloxy-carbonyls,1-(p-biphenyl)-1-methylethoxy-carbonyl, and 9-fluorenylmethyloxycarbonyl(Fmoc); aliphatic carbamate types such as tert-butyloxycarbonyl (tBoc),ethoxycarbonyl, diisopropylmethoxycarbonyl, and allyloxycarbonyl; cyclicalkyl carbamate types such as cyclopentyloxycarbonyl andadamantyloxycarbonyl; alkyl types such as triphenylmethyl and benzyl;trialkylsilane such as trimethylsilane; and thiol containing types suchas phenylthiocarbonyl and dithiasuccinoyl Amine protecting groups andprotected amine groups are described in, e.g., C. B. Reese and E.Haslam, “Protective Groups in Organic Chemistry,” J. G. W. McOmie, Ed.,Plenum Press, New York, N.Y., 1973, Chapters 3 and 4, respectively, andT. W. Greene and P. G. M. Wuts, “Protective Groups in OrganicSynthesis,” Second Edition, John Wiley and Sons, New York, N.Y., 1991,Chapters 2 and 3.

Further exemplary amine protecting groups of particular interest includetrihaloacyl groups, such as trihaloacetyl and trihalopropionyl groups(e.g., trichloroacetyl, trifluoroacetyl, trichloropriopionyl,trifluoropriopionyl), and the like, with trihaloacetyl groups being ofinterest.

In one embodiment, the deNAc SA antigen comprising a structure ofFormula I is conjugated to a carrier, e.g., by covalent attachmentthrough a C2 ketone, a C6 aldehyde, C7 aldehyde, or C8 aldehyde asdescribed below (e.g., C2-NH-carrier protein or C6-NH-carrier protein),where the carrier may be present at either the reducing or non-reducingend or both (e.g., through linkage to a residue at the reducing end ofthe derivative, to a residue at the non-reducing end of the derivative,or both). In another embodiment of particular interest, the deNAc SAantigen comprises at least one dimer of Formula I and comprises at thenon-reducing end an N-acylated or de-N-acylated sialic acid residuesubstituted with an acyl amine (e.g., a saturated or unsaturated acylamine, usually a saturated or unsaturated fatty acyl amine, usually asaturated acyl amine (e.g.,. NHC₂₋₁₈, NHC₂₋₁₂, NHC₂₋₁₀, NHC₂₋₈, NHC₄₋₁₂,and the like) (see, e.g., the moiety at the non-reducing end of FormulaeIVa and IVb). These latter embodiments comprising a carrier and/or anacyl amine are of particular interest where the deNAc SA antigencomprises a structure of Formula I, wherein X is H and Y is an acetylgroup, or where X is an acetyl group and Y is H. In another specificembodiment, where the deNAc SA antigen comprises a structure of FormulaI, wherein X is H and Y is an acetyl group, or where X is an acetylgroup and Y is H, the PS derivative is provided in combination with anadjuvant, as described below, where the PS derivative and adjuvant areusually provided in a pharmaceutically acceptable carrier (dry oraqueous diluent).

In one embodiment, the dimer is a disaccharide, where the disaccharidecomprises one or more residues in which the N-acetyl group on the C-5amino group has been removed or, where one of the two residues arede-N-acetylated, the second residue contains an N-acetyl group (but insome embodiments not an N-propionyl group). The disaccharide unitdefining this minimal epitope may be at the reducing end, thenon-reducing end, or within the polysaccharide. Where the deNAc SAantigen is provided as a disaccharide, the composition can have thestructure:

wherein X and Y are independently H, an amine protecting group (e.g., atrihaloacyl group), or a saturated or unsaturated acyl group; preferablyfurther wherein when X is a acyl group (preferably other than apropionyl group), Y is H or an amine protecting group, and when Y isacyl group (preferably other than a propionyl group) X is H or an amineprotecting group. In an embodiment of particular interest, X is anacetyl group and Y is H. Where X and/or Y are an amine protecting group,the compound is referred to herein as a protected deNAc SA antigen,where the protecting groups can be exploited as described above.Exemplary amine protecting groups are those described above. A deNAc SAantigen of Formula II can be further modified to include a carrierand/or an acyl amine, as described above for deNAc SA antigens ofFormula I, particularly where X is H and Y is an acetyl group; or whereX is an acetyl group and Y is H.

DeNAc SA antigens also include those comprising a structure representedby the formula:

where X, Y, and n are as defined above, and R₁ and R₂ are independentlyH or an amine protecting group (e.g., a trihaloacyl group); or an acylgroup (e.g., acetyl group) as described above. A deNAc SA antigen ofFormula III can be further modified to include a carrier and/or an acylamine, with modification of protected deNAc SA antigens being ofinterest, as described above for deNAc SA antigens of Formulae I and II,particularly where X is H and Y is an acetyl group and where X is anacetyl group and Y is H.

In another embodiment, the deNAc SA antigen comprises a structurerepresented by the formulae:

wherein

X₁, X, Y and Z are H, an amine protecting group (e.g., a trihaloacylgroup), or a saturated or unsaturated acyl group, usually an unsaturatedacyl group, usually wherein X₁, X, Y, and Z are 1) H or an amineprotecting group, or 2) a saturated or unsaturated acyl group (usually asaturated acyl group); with the proviso that at least one of X, Y, and Zis H or an amine protecting group; and at least one of X, Y, and Z is asaturated or unsaturated (usually saturated) acyl group; withembodiments of particular interest being those in which at least one ofX, Y, and Z is H or a an amine protecting group; at least one of X, Y,and Z is an acetyl group, and at least one of X, Y and Z is a propionylgroup;

n is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more, usually 5 residuesor greater, more usually about 10 residues or greater (e.g., having adegree of polymerization (Dp) of about 2 to about 60, about 10 to about50, about 30 to about 50, about 10 to 20, or about 12 to about 18, witha Dp of about 2 to about 10 being of particular interest);

R₁ is a saturated or unsaturated acyl amine, usually a saturated orunsaturated fatty acyl amine, usually a saturated acyl amine (e.g.,.NHC₂₋₁₈, NHC₂₋₁₂, NHC₂₋₁₀, NHC₂₋₈, NHC₄₋₁₂, and the like); and

R₂ is a hydroxyl or one or more acylated, amine protected (i.e., havingan amine protecting group, e.g., trihaloacylated), or de-N-acetylatedsialic acid residues as described herein. In one embodiment, R₂ is apolymer of de-N-acetylated sialic acid residues and acylated sialic acidresidues (usually a sialic acid residue having a saturated N-acyl group,e.g,. acetylated sialic acid residues, propionylated sialic acidresidues, and the like).

In one embodiment, the deNAc SA antigens of Formula IVa and IVbcomprises at least one of each of a free amine (or an amine protectinggroup), an acetyl group, and a propionyl group. In this embodiment, thePS derivative can have the structure of Formula V, wherein when X is H,Y and Z are different acyl groups and are either an acetyl group or apropionyl group; when X is an acetyl group, Y and Z are differentmoieties and are either H (or an amine protecting group) or a propionylgroup; and when X is a propionyl group, Y and Z are different moietiesand are either H (or an amine protecting group) or an acetyl group.Exemplary embodiments are set out in FIGS. 23-37.

In another embodiment, the deNAc SA antigens can be described ascomprising at least one trimer having a structure represented by theformula:

wherein

X, Y and Z are independently H, an amine protecting group (e.g., atrihaloacyl group), or a saturated or unsaturated acyl group (usually asaturated acyl group); usually where X, Y and Z are independently 1) Hor an amine protecting group, or 2) a saturated or unsaturated acylgroup, usually a saturated acyl group; with the proviso that at leastone of X, Y, and Z is H or an amine protecting group; and at least oneof X, Y, and Z is a saturated or unsaturated acyl group, usually asaturated acyl group; with embodiments of particular interest beingthose in which at least one of X, Y, and Z is H or an amine protectinggroup; at least one of X, Y, and Z is an acetyl group; and at least oneof X, Y and Z is a propionyl group;

n is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more, usually about 4residues or greater, more usually about 10 residues or greater (e.g.,having a degree of polymerization (Dp) of about 2 to about 60, about 10to about 50, about 30 to about 50, about 10 to 20, or about 12 to about18, with a Dp of about 2 to about 10 being of particular interest).

In one embodiment, the deNAc SA antigen has a mixed acyl structurewherein each trimer comprises at least one of each of a free amine, anacetyl group, and a propionyl group. In this embodiment, the deNAc SAantigen has the structure of Formula V, wherein when X is H, Y and Z aredifferent acyl groups and are either an acetyl group or a propionylgroup; when X is an acetyl group, Y and Z are different moieties and areeither H or a propionyl group; and when X is a propionyl group, Y and Zare different moieties and are either H or an acetyl group.

DeNAc SA antigens include acyl derivatives having saturated orunsaturated, usually saturated, alkyl groups of C₁-C₄, usually C₁-C₃,including, for example acetyl, propionyl, isopropyl, butionyl, and thelike. DeNAc SA antigens further include mixed acyl derivativescontaining one or more de-N-acylated sites, where the deNAc SA antigensinclude different saturated or unsaturated, usually saturated, acylgroups.

DeNAc SA antigens further include those containing, a lactone moiety, acyclic sialic acid moiety, or other sialic acid derivative in additionto or in lieu of one or more sialic acid moieties of a deNAc SA antigendescribed herein. For example, deNAc SA antigens having a lactone moietycan comprise the structure:

where X, Y and n are defined as above. DeNAc SA antigens having alactone moiety can be present in a heteropolymer comprising one or morepolymers (e.g,. dimers, trimers) having a structure as described herein.

In another example, the deNAc SA antigen comprises a cyclic imine and/orreduced to a cyclic secondary amine moiety (e.g.,.1-(4-Hydroxy-5-hydroxymethyl-pyrrolidin-2-yl)-ethanone) in lieu of asialic acid moiety can comprise the structure:

where X and n are defined as above. DeNAc SA antigens having a cyclingimine or cyclic secondary amine moiety can be present in a heteropolymercomprising one or more polymers (e.g,. dimers, trimers) having astructure as described herein.

Where the deNAc SA antigen is provided as a single unit of the epitope(i.e., two residues as set out above, or three residues as describedbelow), the deNAc SA antigen is normally covalently attached to acarrier (e.g., a protein carrier). In general, and particularly wherethe deNAc SA antigen is a disaccharide (e.g., as shown in FIG. 11),trisaccharide, or other molecule of 3 or fewer residues, the deNAc SAantigen can be coupled through the C2 ketone or, after periodatetreatment, the C6 aldehyde by reductive amination to a carrier protein(e.g., C2-NH-carrier protein or C6-NH-carrier protein). In otherembodiments, the amine is coupled to aldehydes at C7, C6, and/or C8(see, e.g., FIGS. 20-22), which likely is a result of incompleteoxidation. Coupling to C7 is most common, with coupling to C6 and C8being less common.

DeNAc SA antigens further include those having one or more residueshaving attached lipid moieties (such as in described in U.S. Pat. No.6,638,513). DeNAc SA antigens also include those having one or moreresidues having attached N-fatty acyl groups (e.g. N-lauroyl, N-oleoyl,and the like). Of particular interest are deNAc SA antigens in whichN-fatty acyl-containing residues constitute, for example, 50% of sialicresidues of a deNAc SA antigen sialic acid polymer or less such that theresulting deNAc SA antigens are still soluble in water. DeNAc SAantigens also include those having one or more amidated sialic acidresidues, which residues have an alkyl secondary amine, usually at anon-reducing end of a polymer of a deNAc SA antigen. DeNAc SA antigenshaving one or more amidated sialic acid residues can be prepared by, forexample, coupling fatty amines (e.g. dodecyl amine, oleoyl amine, andthe like) to a C1 carboxyl group by nucleophilic substitution. Ofparticular interest are deNAc SA antigens in which such C1 amidederivatives constitute, for example, about 50% of residues or less ofthe deNAc SA antigen. DeNAc SA antigens further include those conjugatedto a carrier at either the reducing or non-reducing end or both (e.g.,through linkage to a residue at the reducing end of the derivative, to aresidue at the non-reducing end of the derivative, or both).

The deNAc SA antigens can be homopolymers or heteropolymers of 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35,40, 45, 50, 55, 60 or more dimeric epitope units (defining the minimalepitope) as described above, which dimeric units can be adjacent orseparated by monomers or polymers of sialic acid residues or derivativesthereof. In some embodiments, the N-acylated residues of the deNAc SAantigen comprises represents less than 90%, less than 85%, less than84%, less than 80%, less than 75%, less than 70%, less than 60%, or lessthan 55% of the total residues of the compound.

In other embodiments the ratio of de-N-acetylated residues to N-acylatedresidues is 1:1, 2:1, 3:1, 4:1, or 5:1 or more. In specific embodiments,the ratio of de-N-acetylated residues to N-acetylated residues is 1:1,2:1, 3:1, 4:1, or 5:1 or more. In further specific embodiments, theratio of de-N-acetylated residues to N-propionylated residues is 1:1,2:1, 3:1, 4:1, or 5:1 or more. In other specific embodiments, the ratioof de-N-acetylated residues to N-alkylated residues is 1:1, 2:1, 3:1,4:1, or 5:1 or more. In another specific embodiment, the ratio ofde-N-acetylated residues to N-acetylated residues is 1:1, 2:1, 3:1, 4:1,or 5:1 or more.

DeNAc SA antigens can be provided as a composition that is homogenous orheterogenous with respect to the deNAc SA antigen contained therein. Forexample, the invention contemplates compositions comprising deNAc SAantigens that are homogenous or heterogenous with respect to one or moreof dimeric epitope structure, position of the dimeric epitope within thedeNAc SA antigen, presence or absence of a conjugated carrier protein,Dp, molecular weight, ratio of de-N-acylated to N-acylated residues,degree of N-acylation (e.g., degree of N-acetylation orN-propionylation), and the like.

It will be understood that the deNAc SA antigens may be modified toprovide a variety of desired attributes, e.g. improved pharmacologicalcharacteristics, while increasing or at least retaining substantiallyall of the antigenicity or immunogenicity of the unmodified deNAc SAantigen. For instance, a PS can be modified by extending, decreasing thenumber of residues in the polymer (e.g., so as to provide for differingdegrees of polymerization (Dp)). By “Dp” is meant the number of residuesof a polymer.

Substitutions with different residues, either naturally-occurring ornon-naturally occurring, can also be made, e.g., as a result of chemicalmodification during de-N-acetylation, N-acylation, and the like. Forexample, the deNAc SA antigens described herein can be modified by alipid moiety (as described in, for example, Examples 1 and 5 below, andin U.S. Pat. No. 6,638,513 (Seid)), conjugated to a carrier (e.g., ateither the reducing or non-reducing end), and may comprise lactone,cyclic sialic acid, imine and reduced imine structures. In anotherexample, the deNAc SA antigens can be modified by attachment of anN-fatty acyl groups (e.g. N-lauroyl, N-oleoyl, and the like). In furtherexample, the deNAc SA antigens can include one or more sialic acidresidue having an alkyl secondary amine (e.g., C1 amide derivatives),which can be prepared by, for example, coupling fatty amines (e.g.dodecyl amine, oleoyl amine, and the like) to a C1 keto group bynucleophilic substitution.

The deNAc SA antigen (e.g., de-N-acetylated PS) employed in the subjectinvention need not be identical to those disclosed in the Examplessection below, so long as the subject de-N-acetylated PS are able toinduce an immune response in a host that provides for production ofantibodies that selectively bind N. meningitidis capsularpolysaccharide, with little or no significant binding to host antigens(e.g., to host polysialic acid (PSA)). Thus, one of skill will recognizethat a number of derivatives (described in more detail below), can bemade without substantially affecting the activity of the de-N-acetylatedPS.

Methods of Making de-N-acetylated SA Antigens

As described below in more detail, the present disclosure providesmethods for producing deNAc SA antigens. In one embodiment deNAc SAantigens are produced by chemical modification of a bacterialpolysaccharide. In another embodiment, deNAc SA antigens are producedusing a biosynthetic method involving culturing bacteria (Neisseriameningitidis group B or Esherichia coli K1) or a mammalian cell in thepresence of a trihaloacetyl compound, followed by chemical modificationof a PS derivative intermediate compound expressed on the cell surface.Each of these are described in more detail below.

Production of de-N-acetylated SA Antigens Using Bacterial PS

In one embodiment, deNAc SA antigens can be produced by de-N-acetylationof a PS of N. meningitidis or E. coli K1, or other suitable source ofbacterial PS, followed by partial re-N-acylation. Partial re-N-acylationprovides for production of a de-N-acetylated PS derivative having fewerthan 90%, fewer than 85%, fewer than 84%, fewer than 80%, fewer than75%, fewer than 70%, fewer than 60%, or fewer than 55%, usually about10%, about 15%, about 16%, about 20%, about 25%, about 30%, about 40%,or about 45% N-acylated residues relative to the total residues of thecompound. In this regard, the invention provides for control of thelevel of acylation of the final product, so as to provide ade-N-acetylated PS having a desired level of acylation. In general,reacylation is controlled or prevented by limiting the amount ofacylating reagent.

The deNAc SA antigens can also be produced also by de-N-acetylation of aPS of N. meningitidis or E. coli Kl, or other suitable source ofbacterial PS, followed by re-N-acylation with a mixture of amineprotected group and acyl groups (e.g., trihaloacetyl and acetyl groups)in a desired ratio such that the PS derivative contains fewer than 90%,fewer than 85%, fewer than 84%, fewer than 80%, fewer than 75%, fewerthan 70%, fewer than 60%, fewer than 55% amine protected residues,usually about 10%, about 15%, about 16%, about 20%, about 25%, about30%, about 40%, or about 45% amine protected residues (e.g.,N-trihaloacylated residues) relative to the total residues of thecompound (where the compound generally contains at least 10 or at least20 residues). The level of acylation of the final product after removalof the amine protecting group can be controlled to reduce undesirableside reactions with free amino groups, so as to provide a deNAc SAantigen having a desired level of acylation. Removal of the amineprotecting groups for a free amine at the deprotected residue. Ingeneral, the proportion of de-N-acetyl residues is controlled bylimiting the amount of amine protecting reagent (e.g, the amount of atrihaloacylting reagent).

DeNAc SA antigens can also be produced by biosynthesis of a PS of N.meningitidis or E. coli K1, or other suitable source of bacterial PS, inwhich the bacterial growth media is supplemented with a mixture of anamine-protected mannosamine (e.g., N-trihaloacyl mannosamine) and acylmannosamine (e.g., N-trihaloacetyl and N-acetyl mannosame) in a desiredratio such that the deNAc SA antigen expressed by the bacteria containsfewer than 90%, fewer than 85%, fewer than 84%, fewer than 80%, fewerthan 75%, fewer than 70%, fewer than 60%, or fewer than 55%amine-protected (e.g., N-trihalo acylated) residues relative to thetotal residues of the PS produced. The level of acylation of the finalproduct after removal of the amine protecting group is controlled toreduce undesirable side reactions with free amino groups, so as toprovide a deNAc SA antigen having a desired level of acylation. Ingeneral, the proportion of de-N-acetyl residues is controlled bylimiting the amount of amine-protected mannosamine reagent (e.g.,N-trihalo acetyl mannosamine).

PS, including NmB PS and E. coli K1, are exemplary molecules suitablefor use in the PS derivatives and conjugates and other molecules in theinvention, and such starting materials are known in the art, as aremethods for their isolation and conjugation to a carrier.

DeNAc SA antigens can be generated through any conventional meanssuitable. For example, in one embodiment, deNAc SA antigens can beproduced by de-N-acetylation of a PS, which can be accomplished bycontacting a native PS with a basic aqueous medium at elevatedtemperatures, for example about 90° C. to about 110° C., and at a pH ofabout 13 to about 14 (e.g., in sodium hydroxide about 2M concentration).Alternatively, hydrazine in aqueous solution may be used. The degree ofN-deacetylation at this stage may vary, with at least about 85%, about90%, about 95%, or about 99% up to about 100% de-N-acetylation being ofinterest. The de-N-acetylated product can be recovered by, for example,cooling, neutralizing, purification if desired, and lyophilization.

The non-aqueous and biosynthetic production methods are described inmore detail below, as well as in the Examples.

Non-Aqueous Production Methods

In one embodiment, de-N-acetyl sialic acid antigens can be producedthrough chemical modification of a PS in a polar protic organic solventcontaining less than 5% water. Aqueous solution-based methods used toprepare NmB PS derivatives (as in, for example, Example 1) producerelatively small amounts of material that is reactive with protectivenon-autoreactive mAbs (e.g. SEAM 2,3). Without being held to theory,this low yield results from one or more of the failure to remove allN-acetyl groups as described above, the failure to quantitativelycontrol the amount of re-N-acylation because of poor reactivity of thePS amino groups (intramolecular COO⁻and NH₃ ⁺ charge pairing), competinghydrolysis of the acylating reagent, and/or oxidation of the amino groupby periodate when preparing non-reducing end aldehydes.

Performing acylation of PS in a polar protic organic solvent, and, wheredesired, in the presence of a small amount of water (e.g., formamide,mixed formamide/2.5% water, and the like), protecting amino groups(e.g., with a trihaloacyl (e.g., trichloroacetyl or trifluoroacetyl)amide) which is later removed to generate predictable fractions ofde-N-acetyl residues, and use of a strong base (e.g., sodium hydroxideor methoxide) during the acylation step to ensure amino group reactivityprovides for improved yields and better control of the fraction ofresidues that a de-N-acetylated).

The organic solvent can be any suitable solvent, usually a polar proticor aprotic organic solvent. Exemplary such solvents include formamide,dimethylformamide, mixed formamide/dimethlformamide, and the like ormixtures of organic solvent and a small percent of water (typically atleast about 2% or 2.5% water, but usually less than 10%, less than5%).Water is added as necessary to ensure solubility of the components,particularly of the PS.

The amine groups of the molecule are protected by modifying them with asuitable amine protecting group. Exemplary amine protecting groups aredescribed above, and include, without limitation, a carbamate or amide,including N-alkyl and N-aryl amines, imine derivatives, enaminederivatives, N-sulfonyl, and the like. In one embodiment of particularinterest, the amine protecting groups is a trihaloacyl amide, usuallytrihaloacyl groups of C₂-C₁₂, more usually C₂-C₁₀ more usually C₂-C₈,more usually C₂-C₆, most usually a trihaloacetyl or trihalopropionyl,protecting group. Such protecting groups can be selected for stabilityat pH 8 or lower, stability in the presence of periodate, and/or ease ofremoval as described below. In general, amine protecting group preventsN-oxidation in the presence of periodate. The form of the deNAc SAantigen produced after this protecting step is referred to herein as the“protected deNAc SA antigen”, “protected acylated deNAc SAantigen”,“protected PS derivative” or “protected acylated PSderivative”, wherein the compound comprises one or more amine protectinggroups (e.g., trihaloacyl-protected amine groups).

In general, production of a protected deNAc SA antigen is accomplishedby contacting an at least partially de-N-acetylated PS molecule with anamine protecting group reagent and an acylating reagent in the presenceof an organic solvent as described above. The amine protecting reagentcan be, for example, a trihaloacylating reagent, e.g., trihaloacceticanhydride or alkyl trihaloacetic esters being of particular interest(e.g., trichloroacetic anhydride, trifluoroacetic anhydride, ethyltrifluoracetyl ester, or ethyl trichloroacetyl ester, and the like).Acylating reagents provide an activated acyl group, wherein theactivated acyl group is usually an acetyl group or propionyl group, moreusually an acetyl group. In some embodiments, the trihaloacylatingreagent and acylating reagents are contacted with the de-N-acetylated PSmolecule as a mixture.

The relative amounts of trihaloacylating reagent and acylating reagentin the mixture are provided so that the end product of the protectingstep contains the desired ratio of trihaloacylated residues and acylatedresidues, wherein the trihaloacylated groups will generally be removedto provide a free amine in the final product. For example, where theratio of free amines to acylated residues in the final deNAc SA antigenproduct is to be about 1:10, 1:4, or 1:1, the ratio of trihaloacylatingreagent to acylating reagent is about is present in the mixture at aratio of about 1:10, 1:4, or 1:1. Stated differently, the amount oftrihaloacylating reagent in the mixture is roughly equal to the fractionof de-N-acetyl groups desired in the final deNAc SA antigen productafter deprotection (e.g., 10%, 25%, 50%, and the like). The acylatingreagent can also be provided as a mixture of different activated acylgroups (e.g., acetyl, propionyl) so as to provide for a desired ratio ofdifferently acylated groups in the PS derivative. For example, where thedeNAc SA antigen is to have a ratio of acetylated residues topropionylated residues of 2:1 or 1;1, the acylating agents for activatedacetyl and propionyl groups is provided in the same or similar ratio inthe acylating agent mixture.

After the protecting step, the protected deNAc SA antigen can then bemodified as desired, e.g., by conjugation to a desired carrier, e.g,. byperioidiation followed by reductive amination. The protecting groups canthen be removed (e.g. by hydrolysis or reduction) to leave a free amine,thus providing the final deNAc SA antigen. The amine protecting groupscan be removed by either hydrolysis using a strong aqueous base (e.g.,pH 9 or greater), by reduction (e.g., with sodium borohydride), or bythe amine added during the preparation of conjugates by reductiveamination (see, e.g., Example 5). The deNAc SA antigen can then beisolated according to methods well known in the art.

The nonaqueous production methods can be desirable for a number ofdifferent reasons. First, performing the acylation reactions in anorganic solvent provides greater flexibility in the type of acyl groupsthat can be used. For example, the use of an organic solvent facilitatesuse of fatty acyl groups of greater than 4 carbons which can posechallenges with respect to solubility in aqueous systems, as well ashighly reactive activated acyl groups (e.g., trifluoroacetyl andtrichloroacetyl). The reaction in organic solvent also provides greatercontrol over the degree of acylation, since there is no or minimalcompeting reaction with water and OH⁻ to deplete the reagent. As aresult, the acylation reactions with the polysaccharide can be designedso that they proceed to completion.

The non-aqueous approach also allows the use of protected amine groups.When left unprotected, the polysaccharide amine groups may participatein other undesired reactions such as oxidation in the presence ofperiodate and intramolecular reactions with activated carboxyl groups,or with aldehydes introduced at the non-reducing end and the reducingend ketone. Trifluoroacetyl or trichloroacetyl are preferred protectinggroups since they are stable at pH less than about 8, stable in thepresence of periodate, and can easily be removed in aqueous base or byreduction with sodium borohydride to produce deNAc SA antigen containingde-N-acetyl residues where the percentage of de-N-acetyl residues iscontrolled by the amount of amine derivatized with protecting groups.

Biosynthetic Methods of deNAc SA Antigen Production Using Bacteria

In another embodiment, deNAc SA antigens are generated by culturing N.meningitidis bacteria, particularly Group B bacteria, in the presence ofone or more N-acyl mannosamine derivatives and under conditions topromote production of deNAc SA antigen having N-acyl sialic acidresidues. This can be accomplished by including n the bacterial culturemedium a mannosamine derivative having a desired N-acyl group.

In one embodiment, the N-acyl mannosamine derivative is a mannosaminecomprising an amine protecting group (a “protected mannosamine” or“amine protected mannosamine”), exemplified herein by N-trihaloacylmannosamines, to accomplish “feeding of the mannosamine derivative tothe bacteria. Exemplary amine protected mannosamines suitable for use inthe invention include any amine protected mannosamine that canincorporated into the bacterium's PS synthetic pathway to provide forproduction of a protected deNAc SA antigen. Exemplary amine protectedmannosamine reagents include N-trihaloacyl mannosamine, e.g.,N-trihaloacetyl mannosamine (e.g., N-trichloroacetyl mannosamine,trifluoroacetyl mannosamine), N-formyl mannosamine, and the like). Inaddition to the amine-protected mannosamine, the culture mediumgenerally also includes an N-acetyl mannosamine, to provide for a deNAcSA antigen having both protected sialic acid residues and N-acetylatedsialic acid residues.

Without being held to theory, when cultured in the presence of the amineprotected mannosamine, bacterial enzymes involved in capsulebiosynthesis incorporate the amine protected mannosamine into sialicacid, which is then incorporated into capsule polysaccharide. Standardfermentation and purification methods can be used to generate aprotected deNAc SA antigen containing a desired fraction of monomershaving attached protecting groups. The deNAc SA antigen containing theseprotecting groups can be of the structures described above, for example.

In a related embodiment, where a deNAc SA antigen having mixed N-acylsialic acid residues is desired, the culture medium includes mixedN-acyl mannosamine reagents. For example, the N-acyl mannosamine cancomprise saturated or unsaturated acyl groups, usually saturated acylgroups, of from C₁-C₅, more usually C₂-C₅, more usually C₂-C₄, moreusually C₂-C₃, with acetyl or propionyl groups being of particularinterest. Culturing the bacteria in the presence of such mixed N-acylmannosamine reagents can provide for production of a deNAc SA antigenhaving mixed N-acyl sialic acid residues, e.g,. N-acetyl sialic acid,N-propionyl sialic acid, and the like. In one embodiment of particularinterest, the bacteria is cultured in the presence of a mixture of aprotected mannosamine (e.g., a N-trihaloacyl mannosamine) and N-acylmannosamines (e.g,. a mixture of N-acetyl mannosamine and N-propionylmannosamine)

In one embodiment, a N. meningitids bacteria, preferably a Group Bstrain, is cultured in the presence of a mixture of an N-acylmannosamine (e.g., N-acetyl mannosamine) and a N-trihaloacylmannosamine. In other embodiments, the bacteria is a non-encapsulatedstrain, and can be a strain that is defective in PS capsule synthesis inthe absence of supplemental N-acetyl mannosamine in the culture medium(e.g., due to a defect in one or more enzymes such that the bacteriacannot synthesize capsule PS unless the growth media is supplementedwith N-acetyl mannosamine). For example, the strain can be defective inan N-acetyl-D-glucosamine-6-phosphate 2 epimerase, such as in the NmBstrain M7.

The relative amounts of mannosamine reagents in the culture (e.g., theratio of N-trihaloacyl mannosamine and N-acetyl mannosamine) areprovided so that the biosynthetic end product contains the desired ratioof different sialic acid residues and/or derivatives in the deNAc SAantigen (e.g., trihaloacylated residues and acylated residues on thedeNAc SA antigen). In general, the protecting groups (e.g,. thetrihaloacylated groups) are removed to provide a free amine in the finaldeNAc SA antigen product. For example, where the ratio of free amines toacylated residues in the final deNAc SA antigen product is to be about1:10, 1:4, or 1:1, the ratio of N-trihaloacyl mannosamine to mannosamineis about 1:10, 1:4, or 1:1. Stated differently, the amount ofN-trihaloacyl mannosamine in the culture is roughly equal to thefraction of de-N-acetyl sialic acid groups desired in the final deNAc SAantigen product after deprotection (e.g., 10%, 25%, 50%, and the like).

Similarly, the relative amounts of “unprotected” N-acyl mannosamines(mannosamines that do not contain an amine protecting group, but whichcan comprise, for example, an acetyl or proprionyl group as the N-acylgroup) in the culture can be provided so as to provide for a desiredratio of differently acylated sialic acid residues in the deNAc SAantigen. For example, where the deNAc SA antigen is to have a ratio ofacetylated residues to propionylated residues of 2:1 or 1;1, N-acetylmannosamine and N-propionyl mannosamine is provided in the same orsimilar ratio in the culture.

The deNAc SA antigens can then isolated from the bacteria using methodsknown in the art. Where the deNAc SA antigen contains an amineprotecting group, such deNAc SA antigen are especially suitable forgenerating a deNAc SA antigen having further modification, e.g., aconjugate (e.g,. by periodate oxidation of the non-reducing end) ormodifying a sialic acid residue to provide an alkyl secondary amine,particularly a C1 amide, at a non-reducing end of the polymer(polysaccharide). After modification is completed, the trihaloacylprotecting groups can be removed as described above. For example, theprotecting groups can be removed by reductive amination (e.g., withsodium cyanoborohydride) or further reduction (e.g., with sodiumborohydride or treatment with base at pH 9 or greater) to provide a freeamine.

Fragments, Re-Acylation, and Other Modifications

Where the deNAc SA antigen is produced by chemical modification of PS,fragments of PS are usually produced as a result of N-deacetylation,which fragments generally have an average molecular weight ranging fromabout 3,000 to about 50,000 Daltons. While the invention contemplatesdeNAc SA antigen that are full-length derivatives of PS as well asfragments, deNAc SA antigens of PS fragments are also contemplated.

Where desired, re-acylation to provide the deNAc SA antigen can becarried out by resuspending de-N-acetylated PS in an aqueous medium ofabout pH 8 to 9 (e.g., in sodium hydroxide), followed by addition of anappropriate acyl anhydride. In one embodiment, both the polysaccharideand acylating agent (e.g. acetyl anhydride or propionic anhydride) areprovided in an organic solvent/water mixture (e.g., 2% (vol./vol.) waterin formamide or dimethylformamide). This embodiment in particularprovides for more controlled levels of reacylation. The method of theinvention involves use of less than 1 molar equivalent, less than 0.75mole equivalent, less than 0.5 mole equivalent, less than 0.25 moleequivalent, less than 0.1 mole equivalent, less than 0.05 moleequivalent, less than 0.025 mole equivalent, or as little as 0.02 moleequivalent of acid anhydride or acylating agent (e.g. acyl-active estersuch as O-acyl hydroxysuccinimide).

O-acyl groups can be removed by increasing the pH to about 12. The pH isthen lowered to about 8 (e.g., by addition of hydrochloric acid), andthe derivative purified as desired, e.g., by dialysis. The reactionproducts can be further purified and lyophilized as desired.

The degree of N-acylation of the resulting deNAc SA antigen is generallyless than 90%, less than 85%, less than 84%, less than 80%, less than75%, less than 70%, less than 60%, or less than 55%, usually greaterthan 10%, 15%, 16%, 25%, 30%, 40%, or 45%. The molecular weight of thepolysaccharide of the deNAc SA antigen can vary, with deNAc SA antigensproduced from PS generally ranging in molecular weight from about 0.5kDa (e.g., a disaccharide) to 80 kDa, about 1 kDa to about 70 kDa, about2 kDa to about 60 kDa, about 3 kDa to about 50 kDa, about 5 kDa to about25 kDa, about 10 kDa to 80 kDa, about 20 kDa to 60 kDa, about 30 kDa toabout 50 kDa, usually about 0.5 kDa to about 10 kDa.

Methods of Making deNAc SA Antigens from Gangliosides

In general, deNAc SA antigens can be produced from gangliosides bybiosynthesis of a ganglioside derivative in a mammalian cell (e.g., acancerous mammalian cell), or other suitable source, by culturing thecell in growth media supplemented with a mixture of an amine-protectedmannosamine (e.g., N-trihaloacyl mannosamine) and acyl mannosamine(e.g., N-trihaloacetyl and N-acetyl mannosame). The amine-protectedmannosamine and acyl mannosamine can be provided in the culture mediumin a desired ratio such that the ganglioside derivative expressed by thecell contains fewer than 90%, fewer than 85%, fewer than 84%, fewer than80%, fewer than 75%, fewer than 70%, fewer than 60%, or fewer than 55%,usually greater than 10%, 15%, 16%, 25%, 30%, 40%, or 45%.amine-protected (e.g., N-trihalo acylated) residues relative to thetotal residues of the ganglioside produced.

This method can provide for control of the level of acylation of thefinal product after removal of the amine protecting group and reducingor avoiding undesirable side reactions with free amino groups, so as toprovide a de-N-acetylated ganglioside having a desired level ofacylation. In general, the proportion of de-N-acetyl residues iscontrolled by limiting the amount of amine-protected mannosamine reagent(e.g., N-trihalo acetyl mannosamine). The de-N-acetylated product can berecovered from the cells by any convention method, for example, cooling,neutralizing, purification if desired, and lyophilization.

The biosynthetic production methods are described in more detail below,as well as in the Examples.

Biosynthetic deNAc SA Antigen Production by Production of a GangliosideDerivative in a Mammalian Cell

In one embodiment, deNAc SA antigens are generated by culturing amammalian cell, (e.g., a cancerous cell of a desired tissue type orcancer type (e.g., a cell of a primary tumor, a metastais of a tumor, ora tumor cell line, e.g., a melanoma cell line (e.g., SK-MEL-28 cellline)), in the presence of one or more N-acyl mannosamine derivativesand under conditions to promote production of ganglioside derivativeshaving N-acyl sialic acid residues. This can be accomplished byincluding in the cell culture medium a mannosamine derivative having adesired N-acyl group.

Any suitable mammalian cell which provides for ganglioside production ata desired level can be used in the biosynthetic methods of theinvention. Such cells can naturally express gangliosides, or can beengineered to express or overexpress a ganglioside, e.g., GD3 (see,e.g., CHO cells transfected with GD3 synthase (ST8Sia-I), described inSatake et al. J. 2003 Biol. Chem. 278:7942-7948). In some embodiments,the cell used in the biosynthetic methods use cancerous cells thatproduce GD3 at an elevated level relative to non-cancerous cells (e.g.,of the same tissue type or origin). Exemplary cells include, but are notlimited to, cells or cell lines of neuroectodermal origin, cancer cellsor cell lines (e.g., SK-MEL-28 cells, SK-MEL-37, M21 cells, MELUR cells,and the like), and the like.

In one embodiment, the N-acyl mannosamine derivative is a mannosaminecomprising an amine protecting group (a “protected mannosamine” or“amine protected mannosamine”), exemplified herein by N-trihaloacylmannosamines, to accomplish “feeding” of the mannosamine derivative tothe cancerous cell. Exemplary amine protected mannosamines suitable foruse in the invention include any amine protected mannosamine that canincorporated into the cells ganglioside synthetic pathway to provide forproduction of a protected ganglioside derivative. Exemplary amineprotected mannosamine reagents include N-trihaloacyl mannosamine, e.g.,N-trihaloacetyl mannosamine (e.g., N-trichloroacetyl mannosamine,trifluoroacetyl mannosamine), N-formyl mannosamine, and the like). Inaddition to the amine-protected mannosamine, the culture mediumgenerally also includes an N-acetyl mannosamine, to provide for aganglioside derivative having both protected sialic acid residues andN-acetylated sialic acid residues.

In a related embodiment, where a ganglioside derivative having mixedN-acyl sialic acid residues is desired, the culture medium includesmixed N-acyl mannosamine reagents. For example, the N-acyl mannosaminecan comprise saturated or unsaturated acyl groups, usually saturatedacyl groups, of from C₁-C₅, more usually C₂-C₅, more usually C₂-C₄, moreusually C₂-C₃, with acetyl or propionyl groups being of particularinterest. Culturing the cancerous cells in the presence of such mixedN-acyl mannosamine reagents can provide for production of a gangliosidederivative having mixed N-acyl sialic acid residues, e.g,. N-acetylsialic acid, N-propionyl sialic acid, and the like. In one embodiment ofparticular interest, the cells are cultured in the presence of a mixtureof a protected mannosamine (e.g., a N-trihaloacyl mannosamine) andN-acyl mannosamines (e.g., a mixture of N-acetyl mannosamine andN-propionyl mannos amine)

In another embodiment, a mammalian cell (e.g., a cancer cell) iscultured in the presence of a mixture of an N-acyl mannosamine (e.g.,N-acetyl mannosamine) and a N-trihaloacyl mannosamine. The relativeamounts of mannosamine reagents in the culture (e.g., the ratio ofN-trihaloacyl mannosamine and N-acetyl mannosamine) are provided so thatthe biosynthetic end product contains the desired ratio of differentsialic acid residues and/or derivatives in the ganglioside derivative(e.g., trihaloacylated residues and acylated residues on the gangliosidederivative). In general, the protecting groups (e.g., thetrihaloacylated groups) are removed to provide a free amine in the finalganglioside derivative product. For example, where the ratio of freeamines to acylated residues in the final de-N-acetylated gangliosidederivative product is to be about 1:10, 1:4, or 1:1, the ratio ofN-trihaloacyl mannosamine to mannosamine is about 1:10, 1:4, or 1:1.Stated differently, the amount of N-trihaloacyl mannosamine in theculture is roughly equal to the fraction of de-N-acetyl sialic acidgroups desired in the final de-N-acetylated ganglioside derivativeproduct after deprotection (e.g., 10%, 25%, 50%, and the like).

Similarly, the relative amounts of “unprotected” N-acyl mannosamines(mannosamines that do not contain an amine protecting group, but whichcan comprise, for example, an acetyl or proprionyl group as the N-acylgroup) in the culture can be provided so as to provide for a desiredratio of differently acylated sialic acid residues in the gangliosidederivative. For example, where the ganglioside derivative is to have aratio of acetylated residues to propionylated residues of 2:1 or 1;1,N-acetyl mannosamine and N-propionyl mannosamine is provided in the sameor similar ratio in the culture.

The deNAc SA antigens produced from the gangliosides can then beisolated from the cells using methods known in the art. Where theganglioside derivative contains an amine protecting group, suchganglioside derivatives are especially suitable for generating aganglioside derivative having further modification, e.g., generating aconjugate (e.g,. by periodate oxidation of the non-reducing end) ormodifying a sialic acid residue to provide an alkyl secondary amine,particularly a C₁ amide, at a non-reducing end of the gangliosidederivative. After modification is completed, the trihaloacyl protectinggroups can be removed as described above. For example, the protectinggroups can be removed by reductive amination (e.g., with sodiumcyanoborohydride) or further reduction (e.g., with sodium borohydride ortreatment with base at pH 9 or greater) to provide a free amine.

In related embodiments, compositions comprising a mammalian cell havinga cell surface trihaloacylated ganglioside derivative, including bothwhole cells and membrane extracts thereof, are contemplated by theinvention. The invention also contemplates trihaloacylated gangliosidederivatives isolated from such cells. In addition, the inventioncontemplates methods of making deNAc SA antigens using such cells. Inrelated embodiments, the invention provides a composition having cellswith cell surface de-N-acetylated gangliosides, and/or membranesobtained from such cells, where the cells or membranes are producedusing the biosynthetic methods described here. These compositions can beused to elicit antibodies specific for de-N-acetylated gangliosidesImmunization protocols available in the art, as well as those describedherein, can be readily adapted to accomplished production of antibodiesof a desired specificity.

DeNAc SA Antigen Conjugates

DeNAc SA antigens, a protected amine deNAc SA antigen, can be conjugatedto a carrier, so as to provide a deNAc SA antigen -carrier complex. Theconjugated antigen-carrier complex can comprise multiple carriermolecules, multiple deNAc SA antigen molecules, or both.

As noted above, the deNAc SA antigen of the conjugate can be provided asa dimer defining a minimal epitope as described above, or as a polymericunit (e.g., two or more dimeric units defining the epitope describedabove). Where the deNAc SA antigen is a polymeric structure, the deNAcSA antigen can be homopolymeric or heteropolymeric. The composition cancomprise additional residues attached at the non reducing terminus,reducing-terminus or both the non-reducing- and reducing-termini of thepolymer or protected amine polymer.

The carrier can be a protein, a peptide, a T cell adjuvant or any othercompound capable of enhancing the immune response. The protein may beselected from a group consisting of but not limited to viral, bacterial,parasitic, animal and fungal proteins. In one embodiment, the carrier isalbumin The carrier can be a tetanus toxoid, diphtheria toxoid,meningococcal outer membrane protein complexes (see, e.g., U.S. Pat. No.4,707,543; U.S. Pat. No. 6,476,201; U.S. Pat. No. 6,558,677), or abacterial outer protein (such as recombinant N. meningitidis porin B).Such carriers may be obtained from biochemical or pharmaceutical supplycompanies or prepared by standard methodology (Cruse, J M (ed.)Conjugate Vaccines in Contributions to Microbiology and Immunology vol.10 (1989)). Synthetic peptides containing T-cell epitopes suitable foruse as a carrier may include “universal” T cell epitope(Panina-Bordignon et al 1989 Eur J Immunol 19:2237) or non-natural PanDR Epitope peptides (PADRE) (del Guercio et al 1997 Vaccine 15:441).Other agents, including other proteins, that can function as carrierswould be known to those of ordinary skill in the art of immunology.

Exemplary methods for conjugation of the deNAc SA antigens include, butare not necessarily limited to, conjugation of PS as described in U.S.Pat. Nos. 4,727,136; 5,811,102 (describing a group B meningococcalunsaturated C₃₋₅ N-acyl derivative polysaccharide conjugate); U.S. Pat.No. 5,969,130; and U.S. Pat. No. 6,080,589. For example, conjugation canbe accomplished by introducing an aldehyde group at the non-reducingend, reducing end, or both of a polysaccharide of a deNAc SA antigen,for use in covalent attachment of one or more carrier proteins. Such canbe accomplished through periodiation by contacting the PS or PSderivative with, for example, sodium meta periodate.

Where a deNAc SA antigen comprises an underivatized amino group, certainrestrictions may be imposed upon the procedures that can be used tocouple the deNAc SA antigen to a carrier, such as a carrier protein. Inthis embodiment, the carrier is generally modified to contain one ormore azide (hydrazide or adipic dihydrazide) groups through the reactionof hydrazide or adipic dihydrazide with the carrier protein activated atcarboxyl groups with EDAC (see, e.g., U.S. Pat. No. 6,632,437). Sincethe pKa of the hydrazide amino group is about 2.5, and since hydrazidesare strong nucleophiles, the imine conjugation reaction can be performedat pH of about 5.5-7.5 at which the primary amines on the carrierprotein and the polysaccharide are substantially completely protonatedand thus less reactive.

DeNAc SA antigen-protein conjugate vaccines can be purified by sizeexclusion chromatography (ToyoPerl HW-45F). The protein concentration isdetermined by Lowry protein assay and the amount of conjugatedpolysaccharide by resorcinol assay (Svennerholm 1957 Biochim biophysActa 24:604). To ensure that the protein and polysaccharide arecovalently linked, the conjugate vaccines are resolved on SDS-PAGE andprotein and polysaccharide are detected separately by Western blot usingpolyclonal anti-carrier protein antisera and anti-PS mAbs to detect thepolysaccharide component.

In one example, where the deNAc SA antigen comprises dimeric epitopes,the deNAc SA antigen can be modified to provide for attachment to acarrier and have the following structure:

where X, Y, and are as defined above, and R₁ is H or an acyl group(e.g., an acetyl group). In other embodiments, R1 is selectedindependently from H; a saturated or unsaturated acyl group (e.g., asaturated or unsaturated C₂₋₁₈ acyl group, a saturated or unsaturatedC₂₋₁₆ acyl group, a saturated or unsaturated _(C2-12) acyl group, asaturated or unsaturated C₂₋₁₀ acyl group, a saturated or unsaturatedC₂₋₈ acyl group, a saturated or unsaturated C₂₋₆ acyl group, a saturatedor unsaturated C₂₋₄ acyl group, a saturated C₂₋₄ acyl group); an N-fattyacyl group (e.g. N-lauroyl, N-oleoyl, and the like); or a fatty amine(e.g. dodecyl amine, oleoyl amine, and the like). In one embodiment R1is a C₄ to C₈ acyl group, such as n-butanoyl, isbutanoyl, n-pentanoyl,n-hexyanol, n-heptanoyl or n-octanoyl (as described in, for example U.S.Pat. No. 5,576,002), or an unsaturated C₃-C₅ acyl group, such as thosedescribed in U.S. Pat. No. 6,350,449.

In another embodiment where the deNAc SA antigen comprises trimericrepeats, the deNAc SA antigen can be modified to provide for attachmentto a carrier and have the following structure:

wherein

X, Y and Z are independently H or an amine protecting group; or asaturated or unsaturated acyl group (usually a saturated acyl group),with the proviso that at least one of X, Y, and Z is H or a trihaloacylgroup; and at least one of X, Y, and Z is a saturated or unsaturatedacyl group, usually a saturated acyl group, with embodiments ofparticular interest being those in which at least one of X, Y, and Z isH (or an amine protecting group), at least one of X, Y, and Z is anacetyl group, and at least one of X, Y and Z is a propionyl group;

n is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more, usually about 4residues or greater, more usually about 10 residues or greater (e.g.,having a degree of polymerization (Dp) of about 2 to about 60, about 10to about 50, about 30 to about 50, about 10 to 20, or about 12 to about18, with a Dp of about 2 to about 10 being of particular interest); and

R₁ is H, an amine protecting group, or an acyl group (e.g., a saturatedacyl group, such as an acetyl group). In other embodiments, R₁ isselected independently from H; an amine protecting group; a saturated orunsaturated acyl group (e.g., a saturated or unsaturated C₂₋₁₈ acylgroup, a saturated or unsaturated C₂₋₁₆ acyl group, a saturated orunsaturated C₂₋₁₂ acyl group, a saturated or unsaturated C₂₋₁₀ acylgroup, a saturated or unsaturated C₂₋₈ acyl group, a saturated orunsaturated C₂₋₆ acyl group, a saturated or unsaturated C₂₋₄ acyl group,a saturated C₂₋₄ acyl group); an N-fatty acyl group (e.g. N-lauroyl,N-oleoyl, and the like); or a fatty amine (e.g. dodecyl amine, oleoylamine, and the like). In one embodiment R1 is a C₄ to C₈ acyl group,such as n-butanoyl, isbutanoyl, n-pentanoyl, n-hexyanol, n-heptanoyl orn-octanoyl (as described in, for example U.S. Pat. No. 5,576,002), or anunsaturated C₃-C₅ acyl group, such as those described in U.S. Pat. No.6,350,449.

Propionyl-Linked or Acetyl-Linked Conjugates

In another embodiment, the invention features a composition comprising adeNAc SA antigen comprising a structure represented by the formula:

wherein X, Y, and Z are independently an acryl group (e.g., N-acryl,methacryl) or haloacetyl group (e.g., bromoacetyl, chloroacetyl),wherein at least one of X, Y, and Z is H, and at least one of X, Y, andZ is a saturated acyl group. The deNAc SA antigen can be optionallyconjugated to a carrier protein or alkyl secondary amine covalentlylinked by reaction with the acryl or haloacetyl group. DeNAc SA antigensin this embodiment generally have one or more such structures positionedwithin the polymer. For example, the structure above can represent, forexample, from about 10% to 100%, from about 25% to 90%, from about 50%to 75% of the deNAc SA antigen.

Propionyl-linked or acetyl-linked deNAc SA antigen conjugates can begenerated by reacting at least partially de-N-acetylated PS (or othersialic acid residue-containing polymer, such as a sialic acid-modifiedprotein or ganglioside) with activated acrylic acid or activatedhaloacetic acid, where the activated acrylic acid or activatedhaloacetic acid is generated by reaction with a carboxyl activatingagent such as a carbodiimide, e.g., EDC(1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride). Theamount of activated acrylic acid or activated haloacetic acid can beselected to a desried level of conjugation, e.g., from about 10% toabout 100%, about 25% to about 80%, about 50% to 75% of the deNAc SA inthe PS.

Exemplary propionyl-linked conjugates comprise a structure representedby the formula:

wherein X is a thiol from a reacted cysteine residue, or an amino groupof a reacted lysine, histidine or arginine residue of a carrier protein,and Y and Z are independently H or a saturated acyl group, wherein atleast one of Y and Z is H and at least one of Y and Z is a saturatedacyl group. It will be understood that deNAc SA antigen conjugatescontemplated here include those in which the carrier is conjugatedthrough an acryl group positioned at Y (with X and Z being either H or asaturated acyl group) or conjugated through an acryl group positioned atZ (with X and Y being either H or a saturated acyl group).

Exemplary conjugates linked to a carrier through reaction with ahaloacetyl group comprise a structure represented by the formula:

wherein X is a thiol from a reacted cysteine residue of a carrierprotein, or an amino group of a reacted lysine, histidine or arginineresidue of a carrier protein, and Y and Z are independently H or asaturated acyl group, wherein at least one of Y and Z is H and at leastone of Y and Z is a saturated acyl group. It will be understood thatdeNAc SA antigen conjugates contemplated here include those in which thecarrier is conjugated through a haloacetyl group positioned at Y (with Xand Z being either H or a saturated acyl group) or conjugated through ahaloacetyl group positioned at Z (with X and Y being either H or asaturated acyl group).

Treatment of deNAc SA Antigen Preparations with Exosialidase

Polysaccharide (PS), oligosaccharide (OS), or other N-acylated sialicacid polymer contaminants that do not contain deNAc SA residues can bedecreased, and thus deNAc SA antigen enriched, in compositionscontaining deNAc SA antigens by treatment with an exosialidase (alsoreferred to as an exoneuraminidase) to promote cleavage of sialic acidresidues in contaminating sialic acid polymers (e.g., as in PS and OS)at the α(2→8)-gylocosidic bond. Suitable exosialidases include theexosialidase of Arthrobacter ureafaciens (e.g., SIALIDASE A™),Clostridium perfringens (e.g, SIALIDASE I™), Vibrio cholerae (e.g.,SIALIDASE V™), Salmonella typhimurium (e.g., SIALIDASE T™), Newcastledisease virus, Hitchner B1 Strain (e.g., SIALIDASE N™), and otherexosialidases that can cleave α(2→8)-glycosidic bonds. Exosialidasessuitable for use are commercially available.

Treament with sialidase can be accomplised by for example, incubation ofthe composition in a buffer (e.g., an alkali acetate buffer, such as asodium acetate buffer) at a suitable pH, where the pH can be selected soas to avoid degradation of the deNAc SA antigen (e.g., PS derivative)and/or hydrolosis of the deNAc SA antigen (e.g., PS derivative) (e.g.,which can result in production of sialic acid derivatives, such ascyclic lactone residues). For example, incubation of the sample at a pHof about 6.5 can provide for exosialidase activity while reducing deNAcSA antigen degradation. Incubation can be for any suitable period, e.g.,several hours (e.g., 5, 10, 12 hours or more) to several days (e.g., 1,2, 3, 4, 5 or more days). Incubation can be performed at any suitabletemperature, including room temperature (e.g., about 37° C.). Where lowpH results in formation of sialic acid derivatives, the composition canbe incubated at an elevated pH (e.g., greater than pH 6.5, usuallygreater than pH10) for a short period of time (e.g., 30 min to 1 hour)in order to hydrolyze, for example, cyclic lactones.

Treatment with exosialidase depletes non-reactive, fully N-acylatedsialic acid polymers (e.g., N-acylated PS) which may be present as acontaminant in deNAc SA antigen preparations, particularly thosepreparations made using a synthetic method such as those describedherein. In this manner, treatment with an exosialidase can provide forenrichment of deNAc SA antigen in a composition. For example, treatmentwith sialidase can provide for a composition with less than 60%, or lessthan 40% by weight N-acylated PS.

Exosialidase-treated deNAc SA antigen can be conjugated to a carrierprotein using any sutiable method. For example, exosialidase-treateddeNAc SA antigen can be conjugated by N-acylation (e.g., using acrylicacid or haloacetic acid), followed by conjugation to a protein carrierof interest.

Immunogenicity of deNAc SA Antigens and deNAc SA Antigen Conjugates

The isolated deNAc SA antigen, with or without further conjugation or inthe presence or absence of a presentation structure, may be immunogenicor, alternatively, the immunogenicity may arise from the conjugation.Methods of measuring immunogenicity are well known to those in the artand primarily include measurement of serum antibody includingmeasurement of concentration, avidity, and isotype distribution atvarious times after injection of the construct. Greater immunogenicitymay be reflected by a higher titer and/or increased life span of theantibodies Immunogenicity may be measured using in vitro bactericidalassays as well as by the ability of sera from immunized animals toconfer passive protection to infection or disease in a suitable animalchallenge model Immunogenicity may be measured in the patient populationto be treated or in a population that mimics the immune response of thepatient population.

One means of determining the immunogenicity of a given substance is tofirst obtain sera of an animal (e.g., mouse) both before immunization,and then after priming with deNAc SA antigen or conjugate, followed byboosting with additional doses. Following this, the strength of thepost-immunization sera binding to a deNAc SA epitope is ascertainedusing an ELISA, and compared to the corresponding results with controlmock-immunized animals

The deNAc SA antigen can prime for an immune response to a deNAc SAantigen conjugate that both reduces production of or avoids productionof auto-antibodies and can provide for enhanced antibody response todeNAc SA antigen conjugate compared to a response of an individual notprimed with the de-N-acetylated PS and who has been vaccinated with thesame PS conjugate

Antigenic Composition Formulations

“Antigen composition”, “antigenic composition” or “immunogeniccomposition” is used herein as a matter of convenience to refergenerically to compositions comprising a deNAc SA antigen, includingdeNAc SA antigen conjugates. Antigen compositions can comprise a deNAcSA antigen, conjugate thereof, or both. Compositions useful foreliciting antibodies against NmB, E. coli K1, or cancer cells,particularly cancer cells, are contemplated by the present invention.

The deNAc SA antigens can be provided in such compositions in anisolated form, or in membranes (e.g., in vesicles, e.g., outer membranevesicle or microvesicles, such as produced from a NmB strain). Where thedeNAc SA antigen is generated using the biosynthetic methods involvingmammalian cells, the deNAc SA antigen can be provided on the surface ofa whole mammalian cell or a membrane or lipid extract of a mammaliancell. Where a whole mammalian cell is used, the mammalian cell willusually be inactivated so as to prevent further proliferation onceadministered to the subject. Any physical, chemical, or biological meansof inactivation may be used, including but not limited to irradiation(e.g., with at least about 5,000 cGy, usually at least about 10,000 cGy,more usually at least about 20,000 cGy); or treatment with mitomycin-C(e.g., usually at least 10 .mu.g/mL; more usually at least about 50μg/mL).

In one embodiment, especially where the deNAc SA antigen was generatedby PS, the deNAc SA antigen composition has been treated with anexosialidase to decrease contaminating PS and OS and enrich for deNAc SAin the composition.

Compositions of the invention (particularly those suitable for use asvaccines) comprise an immunologically effective amount of antigen, aswell as any other compatible components, as needed. By “immunologicallyeffective amount” is meant that the administration of that amount to anindividual, either in a single dose, as part of a series of the same ordifferent antigenic compositions, is effective to elicit an antibodyresponse effective for treatment or prevention of a symptom of acancerous cell having a cell surface-accessible deNAc SA epitope (e.g.,a ganglioside that is at least partially de-N-acetylated). DeNAc SAantigen compostions can be administered to elicit an anti-SEAM 3reactive antigen antibody response in a subject.

The amount administered varies depending upon the goal of theadministration (e.g., to provide for immunotherapy in a human subject,to provide for antibody production for generating hybridomas (e.g., asin a non-human host)), the health and physical condition of theindividual to be treated, age, the taxonomic group of individual to betreated (e.g., human, non-human primate, primate, etc.), the capacity ofthe individual's immune system to produce antibodies, the degree ofprotection desired, the formulation of the vaccine, the treatingclinician's assessment of the medical situation, and other relevantfactors. It is expected that the amount will fall in a relatively broadrange that can be determined through routine trials. Dosage treatmentmay be a single dose schedule or a multiple dose schedule (e.g.,including booster doses). The vaccine may be administered in conjunctionwith other immunoregulatory agents.

The compositions of the invention can be provided in a pharmaceuticallyacceptable excipient, which can be a solution such as an aqueoussolution, often a saline solution, or they can be provided in powderform. The compositions of the invention can comprise a deNAc SA antigenand an adjuvant. Examples of known suitable adjuvants that can be usedin humans include, but are not necessarily limited to, alum, aluminumphosphate, aluminum hydroxide, MF59 (4.3% w/v squalene, 0.5% w/v Tween80, 0.5% w/v Span 85), CpG-containing nucleic acid (where the cytosineis unmethylated), QS21, MPL, 3DMPL, extracts from Aquilla, ISCOMS, LT/CTmutants, poly(D,L-lactide-co-glycolide) (PLG) microparticles, Quil A,interleukins, and the like. For experimental animals, one can useFreund's, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP),N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to asnor-MDP),N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine(CGP 19835A, referred to as MTP-PE), and RIBI, which contains threecomponents extracted from bacteria, monophosphoryl lipid A, trehalosedimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween80 emulsion. The effectiveness of an adjuvant may be determined bymeasuring the amount of antibodies directed against the immunogenicantigen.

Further exemplary adjuvants to enhance effectiveness of the compositioninclude, but are not limited to: (1) oil-in-water emulsion formulations(with or without other specific immunostimulating agents such as muramylpeptides (see below) or bacterial cell wall components), such as forexample (a) MF59™ (WO 90/14837; Chapter 10 in Vaccine design: thesubunit and adjuvant approach, eds. Powell & Newman, Plenum Press 1995),containing 5% Squalene, 0.5% Tween 80, and 0.5% Span 85 (optionallycontaining MTP-PE) formulated into submicron particles using amicrofluidizer, (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5%pluronic-blocked polymer L121, and thr-MDP either microfluidized into asubmicron emulsion or vortexed to generate a larger particle sizeemulsion, and (c) RIBI™ adjuvant system (RAS), (Ribi Immunochem,Hamilton, Mont.) containing 2% Squalene, 0.2% Tween 80, and one or morebacterial cell wall components such as monophosphorylipid A (MPL),trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (DETOX™); (2) saponin adjuvants, such as QS21 or STIMULON™(Cambridge Bioscience, Worcester, Mass.) may be used or particlesgenerated therefrom such as ISCOMs (immunostimulating complexes), whichISCOMS may be devoid of additional detergent e.g. WO 00/07621; (3)Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA);(4) cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6,IL-7, IL-12 (WO99/44636), etc.), interferons (e.g. gamma interferon),macrophage colony stimulating factor (M-CSF), tumor necrosis factor(TNF), etc.; (5) monophosphoryl lipid A (MPL) or 3-O-deacylated MPL(3dMPL) e.g. GB-2220221, EP-A-0689454, optionally in the substantialabsence of alum when used with pneumococcal saccharides e.g. WO00/56358; (6) combinations of 3dMPL with, for example, QS21 and/oroil-in-water emulsions e.g. EP-A-0835318, EP-A-0735898, EP-A-0761231;(7) oligonucleotides comprising CpG motifs (Krieg Vaccine 2000, 19,618-622; Krieg Curr opin Mol Ther 2001 3:15-24; Roman et al., Nat. Med.,1997, 3, 849-854; Weiner et aa., PNAS USA, 1997, 94, 10833-10837; Davisetal, J. Immunol, 1998, 160, 870-876; Chu et aa., J. Exp. Med, 1997,186, 1623-1631; Lipford et al, Ear. J. Immunol., 1997, 27, 2340-2344;Moldoveami el al., Vaccine, 1988, 16, 1216-1224, Krieg et al., Nature,1995, 374, 546-549; Klinman et al., PNAS USA, 1996, 93, 2879-2883;Ballas et al, J. Immunol, 1996, 157, 1840-1845; Cowdery et al, J.Immunol, 1996, 156, 4570-4575; Halpern et al, Cell Immunol, 1996, 167,72-78; Yamamoto et al, Jpn. J. Cancer Res., 1988, 79, 866-873; Stacey etal, J. Immunol., 1996, 157,2116-2122; Messina et al, J. Immunol, 1991,147, 1759-1764; Yi et al, J. Immunol, 1996, 157,4918-4925; Yi et al, J.Immunol, 1996, 157, 5394-5402; Yi et al, J. Immunol, 1998, 160,4755-4761; and Yi et al, J. Immunol, 1998, 160, 5898-5906; Internationalpatent applications WO 96/02555, WO 98/16247, WO 98/18810, WO 98/40100,WO 98/55495, WO 98/37919 and WO 98/525811 i.e. containing at least oneCG dinucleotide, where the cytosine is unmethylated; (8) apolyoxyethylene ether or a polyoxyethylene ester e.g. WO 99/52549; (9) apolyoxyethylene sorbitan ester surfactant in combination with anoctoxynol (WO 01/21207) or a polyoxyethylene alkyl ether or estersurfactant in combination with at least one additional non-ionicsurfactant such as an octoxynol (WO 01/21152); (10) a saponin and animmunostimulatory oligonucleotide (e.g. a CpG oligonucleotide) (WO00/62800); (11) an immunostimulant and a particle of metal salt e.g. WO00/23105; (12) a saponin and an oil-in-water emulsion e.g. WO 99/11241;(13) a saponin (e.g. QS21)+3dMPL+IM2 (optionally+a sterol) e.g. WO98/57659; (14) other substances that act as immunostimulating agents toenhance the efficacy of the composition. Muramyl peptides includeN-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-25acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP),N-acetylmuramyl-L-alanyl-D-isoglutarninyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamineMTP-PE), and the like. Adjuvants suitable for human use are ofparticular interest where the subject is a human.

The antigen compositions may comprise other components, such aspharmaceutical grades of mannitol, lactose, starch, magnesium stearate,sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium,carbonate, and the like. The compositions may contain pharmaceuticallyacceptable auxiliary substances as required to approximate physiologicalconditions such as pH adjusting and buffering agents, toxicity adjustingagents and the like, for example, sodium acetate, sodium chloride,potassium chloride, calcium chloride, sodium lactate and the like. Theconcentration of antigen in these formulations can vary widely, and willbe selected primarily based on fluid volumes, viscosities, body weightand the like in accordance with the particular mode of administrationselected and the patient's needs. The resulting compositions may be inthe form of a solution, suspension, tablet, pill, capsule, powder, gel,cream, lotion, ointment, aerosol or the like.

The concentration of antigens of the invention in the pharmaceuticalformulations can vary widely, i.e. from less than about 0.1%, usually ator at least about 2% to as much as 20% to 50% or more by weight, andwill be selected primarily by fluid volumes, viscosities, etc., inaccordance with the particular mode of administration selected.

Immunization

The deNAc SA antigen (which may be optionally conjugated) can be usedalone or in combination with other vaccines. When used in combination,the various compositions can be provided in the same or differentformulations. Where administered in different formulations, thecompositions can be administered at the same or different dosage regimen(e.g., by the same or different routes, at the same or different time(e.g., on the same or different days)), and the like). In general,administration of the deNAc SA antigen can be performed serially, at thesame time, or as a mixture, as described in more detail below.Preferably, administration is serial, with repeated doses of deNAc SAantigen . Exemplary immunization regimens are described below in moredetail.

In general immunization is accomplished by administration by anysuitable route, including administration of the composition orally,nasally, nasopharyngeally, parenterally, enterically, gastrically,topically, transdermally, subcutaneously, intramuscularly, in tablet,solid, powdered, liquid, aerosol form, locally or systemically, with orwithout added excipients. Actual methods for preparing parenterallyadministrable compositions will be known or apparent to those skilled inthe art and are described in more detail in such publications asRemington's Pharmaceutical Science, 15th ed., Mack Publishing Company,Easton, Pa. (1980).

It is recognized that when administered orally, deNAc SA antigens shouldbe protected from digestion. This is typically accomplished either bycomplexing the deNAc SA antigen with a composition to render itresistant to acidic and enzymatic hydrolysis or by packaging in anappropriately resistant carrier such as a liposome. Means of protectinga compound of interest from digestion are well known in the art.

In order to enhance serum half-life, the antigenic preparations that areinjected may also be encapsulated, introduced into the lumen ofliposomes, prepared as a colloid, or other conventional techniques maybe employed which provide an extended serum half-life of the peptides. Avariety of methods are available for preparing liposomes, as describedin, e.g., Szoka et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), U.S.Pat. Nos. 4, 235,871, 4,501,728 and 4,837,028. The preparations may alsobe provided in controlled release or slow-release forms for release andadministration of the antigen preparations as a mixture or in serialfashion.

Where used as a immunotherapy, the compositions can be administered tosubject that is at risk of disease to prevent or at least partiallyarrest the development of disease and its complications. A subject is“at risk” where, for example, the subject exhibits one or more signs orsymptoms of disease, but which are insufficient for certain diagnosisand/or who has been or may be exposed to conditions that increase theprobability of disease. For example, the antigen compositions can alsobe administered to subject that is at risk of a cancer, has a cancer, oris at risk of metastasis of a cancer having a cell surface deNAc SAepitope (e.g., a cell surface ganglioside that is at least partiallyde-N-acetylated).

An amount adequate to accomplish this is defined as a “therapeuticallyeffective dose.” Amounts effective for therapeutic use will depend on,e.g., the antigen composition, the manner of administration, the weightand general state of health of the patient, and the judgment of theprescribing physician. Single or multiple doses of the antigencompositions may be administered depending on the dosage and frequencyrequired and tolerated by the patient, and route of administration. Ingeneral, immunization is provided to as to elicit an immune response inthe subject. As discussed herein the deNAc SA antigen compositions canprovide the advantage that immunization does not elicit detectableantibodies that significantly cross-react with polysialic acid in thesubject, but that specifically bind a deNAc SA epitope (e.g., on acancerous cell).

Immunization Regimen

DeNAc SA antigens are administered to a host in a manner that providesfor production of selective anti-deNAc SA epitope antibodies. DeNAc SAantigen compositions can be administered serially. First, animmunogenically effective dose of a deNAc SA antigen (which may beconjugated to a carrier, and may be with or without excipients) isadministered to a subject. The first dose is generally administered inan amount effective to elicit an immune response (e.g., activation of Band/or T cells). Amounts for the initial immunization generally rangefrom about 0.001 mg to about 1.0 mg per 70 kilogram patient, morecommonly from about 0.001 mg to about 0.2 mg per 70 kilogram patient,usually about 0.005 mg to about 0.015 mg per 70 kilogram patient.Dosages from 0.001 up to about 10 mg per patient per day may be used,particularly when the antigen is administered to a secluded site and notinto the blood stream, such as into a body cavity or into a lumen of anorgan. Substantially higher dosages (e.g. 10 to 100 mg or more) arepossible in oral, nasal, or topical administration.

After administration of the first deNAc SA antigen composition, atherapeutically effective dose of a second antigen composition (e.g.deNAc SA antigen, optionally conjugated and with or without excipients)can be administered to the subject after the subject has beenimmunologically primed by exposure to the first dose. The booster may beadministered days, weeks or months after the initial immunization,depending upon the patient's response and condition.

An immune response to the first antigen composition may be determined byknown methods (e.g. by obtaining serum from the individual before andafter the initial immunization, and demonstrating a change in theindividual's immune status, for example an immunoprecipitation assay, oran ELISA, or a bactericidal assay, or a Western blot, or flow cytometricassay, or the like) and/or demonstrating that the magnitude of theimmune response to the second injection is higher than that of controlanimals immunized for the first time with the composition of matter usedfor the second injection (e.g. immunological priming) Immunologicpriming and/or the existence of an immune response to the first antigencomposition may also be assumed by waiting for a period of time afterthe first immunization that, based on previous experience, is asufficient time for an immune response and/or priming to have takenplace—e.g. 2, 4, 6, 10 or 14 weeks. Boosting dosages of the secondantigen composition are typically from about 0.001 mg to about 1.0 mg ofantigen, depending on the nature of the immunogen and route ofimmunization.

In certain embodiments, an effective dose of a third deNAc SA antigencomposition (e.g. deNAc SA antigen, optionally conjugated and with orwithout excipients) is administered to the subject after the individualhas been primed and/or mounted an immune response to the second antigencomposition. The third booster may be administered days, weeks or monthsafter the second immunization, depending upon the subject's response andcondition. The existence of priming and/or an immune response to thesecond antigen composition may be determined by the same methods used todetect an immune response to the second antigen composition. Theexistence of priming and/or an immune response to the second antigencomposition may also be assumed by waiting for a period of time afterthe second immunization that, based on previous experience, is asufficient time for an immune response to have taken place—e.g. 2, 4, 6,10 or 14 weeks. Boosting dosages of the second antigen composition aretypically from about 0.001 mg to about 1.0 mg of antigen, depending onthe nature of the immunogen and route of immunization.

The use of a fourth, fifth, sixth or greater booster immunization, usingeither a fourth, fifth or sixth antigen composition or more is alsocontemplated.

In one embodiment, a deNAc SA antigen composition is administered atleast once, usually at least twice, and in some embodiments more thantwice.

In one embodiment, a deNAc SA antigen composition (e.g., de-N-acetylatedPS derivative or de-N-acetylated PS derivative conjugate) isadministered as the first antigen composition so as to prime the immuneresponse. Subsequent antigen compositions administered (e.g., thebooster doses) can be the same or different deNAc SA antigencomposition, or can be an antigenic composition that boosts the primedimmune response to the first antigen composition. Without being held totheory, the initial priming dose of a deNAc SA antigen compositiondirects the host immune response toward production of antibodies thatare minimally cross-reactive with host polysialic acid, and thus awayfrom away from production of such autoreactive antibodies. Once thehost's immune response is primed in this manner, then exposure toantigens that might otherwise elicit an autoimmune response may resultin reduced (including insubstantial or not clinically relevant)production of autoantibodies that cross-react with host polysialic acid.

In one embodiment, the antigen compositions can be administered to amammalian subject (e.g., human) that is immunologically naïve withrespect to a deNAc SA epitope-containing antigen. In other embodiments(which may or may not be related), the subject is a human child aboutfive years or younger, and preferably about two years old or younger,and the antigen compositions are administered at any one or more of thefollowing times: two weeks, one month, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11months, or one year or 15, 18, or 21 months after birth, or at 2, 3, 4,or 5 years of age. Treatment of such younger subjects may be of interestin treatment of certain cancers, such as neuroblastomas.

The deNAc SA antigen composition is to be used as a vaccine,administration can be initiated prior to the first sign of diseasesymptoms, at the first sign of possible disease, or prior to or afterdiagnosis of a primary cancer and/or a metastases of a cancer having acell surface deNAc SA epitope (e.g., a ganglioside that is at leastpartially de-N-acetylated).

Antibody Production

It will be readily apparent that compositions comprising a deNAc SAantigen can be used to produce anti-deNAc SA antigen antibodies,including monoclonal antibodies (mAbs) that can be sutiable for use inantibody-based cancer therapies described herein. Methods for generatingmAbs are well known in the art, and readily adapted for use inproduction of anti-deNAc SA epitope mAbs.

For example, hybridomas for mAb production can be formed by isolatingthe stimulated immune cells from an animal immunized with a deNAc SAantigen (usually a non-human animal), such as those from the spleen ofan immunized animal. These cells are then fused to immortalized cells,such as myeloma cells or transformed cells, which are capable ofreplicating indefinitely in cell culture, thereby producing an immortal,immunoglobulin-secreting cell line. The immortal cell line utilized canbe selected to be deficient in enzymes necessary for the utilization ofcertain nutrients. Many such cell lines (such as myelomas) are known tothose skilled in the art, and include, for example: thymidine kinase(TK) or hypoxanthine-guanine phosphoriboxyl transferase (HGPRT). Thesedeficiencies allow selection for fused cells according to their abilityto grow on, for example, hypoxanthine aminopterinthymidine medium (HAT).

The immortal fusion partners utilized can be derived from a line thatdoes not secrete immunoglobulin. The resulting fused cells, orhybridomas, are cultured under conditions that allow for the survival offused, but not unfused, cells and the resulting colonies screened forthe production of the desired monoclonal antibodies. Colonies producingsuch antibodies are cloned, expanded, and grown so as to produce largequantities of antibody, see Kohler and Milstein, 1975 Nature 256:495(the disclosures of which are hereby incorporated by reference).

Large quantities of mAbs having a desired anti-deNAc SA epitopespecificity can be obtained by identifying secreting hybridomasproducing the desired antibodies, and injecting these hybridoma clonesinto the peritoneal cavity of mice and harvesting the ascites fluidtherefrom. The mice, preferably primed with pristane, or some othertumor-promoter, and immunosuppressed chemically or by irradiation, maybe any of various suitable strains known to those in the art. Theascites fluid is harvested from the mice and the monoclonal antibodypurified therefrom, for example, by CM Sepharose column or otherchromatographic means. Alternatively, the hybridomas may be cultured invitro or as suspension cultures. Batch, continuous culture, or othersuitable culture processes may be utilized. Monoclonal antibodies arethen recovered from the culture medium or supernatant.

Anti-deNAc SA epitope antibodies, including antigen binding fragments ofanti-deNAc SA epitope antibodies, can be produced by geneticengineering. In this technique, as with the standard hybridomaprocedure, antibody-producing cells are sensitized to the desiredantigen or immunogen. The messenger RNA isolated from the immune spleencells or hybridomas is used as a template to make cDNA using PCRamplification. A library of vectors, each containing one heavy chaingene and one light chain gene retaining the initial antigen specificity,is produced by insertion of appropriate sections of the amplifiedimmunoglobulin cDNA into the expression vectors. A combinatorial librarycan be constructed by combining the heavy chain gene library with thelight chain gene library. This results in a library of clones whichco-express a heavy and light chain (resembling the Fab fragment orantigen binding fragment of an antibody molecule). The vectors thatcarry these genes are co-transfected into a host (e.g. bacteria, insectcells, mammalian cells, or other suitable protein production hostcell.). When antibody gene synthesis is induced in the transfected host,the heavy and light chain proteins self-assemble to produce activeantibodies that can be detected by screening with the antigen orimmunogen.

Once obtained, the antibody can be isolated and, where desired,purified, for use in the assays and therapies disclosed herein.Isolation and purification of antibodies can be accomplished usingtechniques well known in the art, and can provide forantibody-containing preparations at least 50% to 60%, by weight, freefrom organic molecules with which the antibody is naturally associatedor with which it is associated during manufacture. Antibody preparationsinclude those that contain antibody in an amount of at least 75%, moreusually at least 90%, and generally at least 99%, by weight.

In one embodiment, the anti-deNAc SA epitope antibody is isolated awayfrom contaminants, especially cationic contaminants, by contacting anantibody suspension (e.g., in a buffer) under conditions of high saltconcentration. Suitable salts include alkali metal salts (e.g., alkalimetal sulfates (e.g, sodium sulfate), alkali metal halides (e.g., sodiumchloride), alkali metal acetate salts (e.g, sodium acetate), and thelike. A “high salt concentration” refers to a salt concentration of atleast about 0.5 M or more up to and including 1 M salt. The high saltsolution containing the antibody is incubated under conditions suitableto separate contaminants from the antibody and for a time sufficient toprovide for disruption of ionic and/or electrostatic bonds that may bepresent between the antibody and cationic or other charged contaminants.Suitable periods of time include, but are not limited to about 12 hrs,16 hrs, 18 hrs or more. The solution may be incubated at any suitabletemperature, e,.g., 4° C., 37° C., etc. The antibody can then beisolated and/or purified from the solution. For example, theantibody-containing solution can be processed to remove precipitates(e.g., by centrifugation), and subjected subjected to further isolationand/or purification techniques to isolate the antibody from thesolution, e.g., by size exclusion chromatography. Antibody-containingfractions can be further purified by dialysis (e.g., against phosphatebuffered solution (PBS)) and filtration. This high salt treatment wasfound to be parituclarly suitable for isolation and/or purification ofSEAM 3 mAb, as it resulted in removal of contaminants that affected SEAM3 mAb activity against cancerous cells presenting cell surface SEAM3-reactive antigen.

Antibody-based Diagnostics and Therapeutics

DeNAc SA antigens (including unconjugated and conjugated forms) can beused to generate antibodies, which antibodies can be used as reagentsfor use in diagnostic assays and in antibody-based therapy. The presentdisclosure provides comprising antibodies that selectively bind a deNAcSA epitope (e.g., as present on a de-N-acetylated ganglioside; N.meningitidis PS, particularly NmB PS; or E. coli K1 PS, and the like).Such antibodies can exhibit little or no detectable binding to humanpolysialic acid (that is, the antibodies are not significantlycross-reactive with PSA on normal (non-cancerous) human tissue). Theanti-deNAc SA epitope antibodies can be monoclonal or polyclonal, andcan be provided with a suitable excipient. In some embodiments theantibodies can be immobilized on a support, or provided in a containersuch as a vial, particularly a sterile vial, optionally labeled for usein a diagnostic or therapeutic method as described in more detail below.

Diagnostics

Antibodies reactive with a deNAc SA epitope can be used to detect deNAcSA antigens in a biological sample obtained from a subject having orsuspected of having cancerous cells having a cell surface accessibledeNAc SA epitope (e.g., a de-N-acetylated cell surface ganglioside)using anti-deNAc SA epitope antibodies in immunodiagnostic techniques.The antigen binding specificity of anti-deNAc SA epitope antibodies canbe exploited in this context, to facilitate detection of deNAc SAepitopes on a cancerous cell in a sample with little or no detectablebinding to host-derived PSA, thereby reducing the incidence of falsepositive results. Such detection methods can be used in the context ofdiagnosis, identification of subject suitable to anti-deNAc SAantigen-based and/or antibody-based therapy where the antibodyspecifically binds an deNAc SA epitope and/or a SEAM 3-reactive antigen,monitoring of therapy (e.g., to follow response to therapy), and thelike.

Suitable immunodiagnostic techniques include, but are not necessarilylimited to, both in vitro and in vivo (imaging) methods. Where themethods are in vitro, the biological sample can be any sample in which adeNAc SA antigen may be present, including but not limited to, bloodsamples (including whole blood, serum, etc.), tissues, whole cells(e.g., intact cells), and tissue or cell extracts. Assays can take awide variety of forms, such as competition, direct reaction, or sandwichtype assays. Exemplary assays include Western blots; agglutinationtests; enzyme-labeled and mediated immunoassays, such as ELISAs;biotin/avidin type assays; radioimmunoassays; immunoelectrophoresis;immunoprecipitation, and the like. The reactions generally includedetctable labels such as fluorescent, chemiluminescent, radioactive,enzymatic labels or dye molecules, or other methods for detecting theformation of a complex between antigen in the sample and the antibody orantibodies reacted therewith.

The assays can involve separation of unbound antibody in a liquid phasefrom a solid phase support to which antigen-antibody complexes arebound. Solid supports which can be used in the practice of the inventioninclude substrates such as nitrocellulose (e.g., in membrane ormicrotiter well form); polyvinylchloride (e.g., sheets or microtiterwells); polystyrene latex (e.g., beads or microtiter plates);polyvinylidine fluoride; diazotized paper; nylon membranes; activatedbeads, magnetically responsive beads, and the like.

Where a solid support is used, the solid support is usually firstreacted with a solid phase component (e.g., an anti-deNAc SA epitopeantibody) under suitable binding conditions such that the component issufficiently immobilized to the support. Sometimes, immobilization tothe support can be enhanced by first coupling the antibody to a proteinwith better binding properties, or that provides for immobilization ofthe antibody on the support with out significant loss of antibodybinding activity or specificity. Suitable coupling proteins include, butare not limited to, macromolecules such as serum albumins includingbovine serum albumin (BSA), keyhole limpet hemocyanin, immunoglobulinmolecules, thyroglobulin, ovalbumin, and other proteins well known tothose skilled in the art. Other molecules that can be used to bindantibodies the support include polysaccharides, polylactic acids,polyglycolic acids, polymeric amino acids, amino acid copolymers, andthe like, with the proviso that the molecule used to immobilize theantibody does not adversely impact the ability of the antibody tospecifically bind antigen. Such molecules and methods of coupling thesemolecules to the antigens, are well known to those of ordinary skill inthe art. See, e.g., Brinkley, M. A. Bioconjugate Chem. (1992) 3:2-13;Hashida et al., J. Appl. Biochem. (1984) 6:56-63; and Anjaneyulu andStaros, International J. of Peptide and Protein Res. (1987) 30:117-124.

After reacting the solid support with the solid phase component, anynon-immobilized solid-phase components are removed from the support bywashing, and the support-bound component is then contacted with abiological sample suspected of containing deNAc SA epitopes undersuitable binding conditions. After washing to remove any non-boundligand, a secondary binder moiety is added under suitable bindingconditions, wherein the secondary binder is capable of associatingselectively with the bound ligand. The presence or absence of thesecondary binder can then be detected using techniques well known in theart.

An ELISA method can be used, wherein the wells of a microtiter plate arecoated with anti-deNAc SA epitope antibody according to the presentinvention. A biological sample containing or suspected of containing adeNAc SA antigen (e.g., a tumor antigen having a deNAc SA epitope, suchas a de-N-acetylated ganglioside), is then added to the coated wells.After a period of incubation sufficient to allow antibody binding, theplate(s) can be washed to remove unbound moieties and a detectablylabeled secondary binding molecule added. The secondary binding moleculeis allowed to react with any captured antigen, the plate washed and thepresence or absence of the secondary binding molecule detected usingmethods well known in the art.

Where desired, the presence or absence of bound deNAc SA antigen from abiological sample can be readily detected using a secondary bindercomprising an antibody directed against the antibody ligands. Forexample, a number of anti-bovine immunoglobulin (Ig) molecules are knownin the art which can be readily conjugated to a detectable enzyme label,such as horseradish peroxidase, alkaline phosphatase or urease, usingmethods known to those of skill in the art. An appropriate enzymesubstrate is then used to generate a detectable signal. In other relatedembodiments, competitive-type ELISA techniques can be practiced usingmethods known to those skilled in the art.

Assays can also be conducted in solution, such that the antibodies anddeNAc SA antigen form complexes under precipitating conditions. Forexample, the antibody can be attached to a solid phase particle (e.g.,an agarose bead or the like) using coupling techniques known in the art,such as by direct chemical or indirect coupling. The antibody-coatedparticle is then contacted under suitable binding conditions with abiological sample suspected of containing deNAc SA antigen to providefor formation of particle-antibody-deNAc SA antigen complex aggregateswhich can be precipitated and separated from the sample using washingand/or centrifugation. The reaction mixture can be analyzed to determinethe presence or absence of antibody-antigen complexes using any of anumber of standard methods, such as those immunodiagnostic methodsdescribed above.

The test sample used in the diagnostics assays can be any sample inwhich a deNAc SA antigen may be present, including but not limited to,blood samples (including whole blood, serum, etc.), tissues, whole cells(e.g., intact cells), and tissue or cell extracts.containing cells(e.g., tissue, isolated cells, etc.), a cell lysate (i.e., a samplecontaining non-intact cells), where each type of sample can containelements of both types (e.g., a sample of cells can contain celllysates, and vice versa). In some embodiments it may be desirable toconduct the assay using a sample from the subject to be diagnosed thatcontains intact, living cells. DeNAc SA antigen detection can then beassessed on an extracellular surface of the cells, and can further beassessed during cell division.

Diagnostic assays can also be conducted in situ. For example, anti-deNAcSA epitope antibodies can be detectably labeled, administered to asubject suspected of having a cancer characterized by cell surfaceexpression of a deNAc SA epitope, and bound detectably labeled antibodydetected using imaging methods available in the art.

The diagnostic assays described herein can be used to determine whethera subject has a cancer that is amenable to therapy using a deNAc SAantigen-based immunotherapy (e.g., deNAc SA antigen vaccine and/oranti-deNAc SA antigen antibody therapy). The diagnostic assays caninform selection of therapy and treatment regimen by a clinician.

In one embodiment, the detection assays involve detection of a SEAM3-reactive antigen in a sample, where the sample can contain Where themethods are in vitro, the biological sample can be any sample in which aSEAM 3-reactive antigen may be present, including but not limited to,blood samples (including whole blood, serum, etc.), tissues, whole cells(e.g., intact cells, i.e., cells that have not been subjected topermeabilization), or cell lysates (e.g, as obtained from treatment of atissue sample). For example, the assay can involve detection of a SEAM3-reactive antigen on cells in a histological tissue sample. Forexample, the tissue sample may be fixed (e.g., by formalin treatment)and may be provided embedded in a support (e.g., in paraffin) or frozenunfixed tissue.

The SEAM 3-reactive antigen can be detected by detection of specificbinding of an antibody, usually a monoclonal antibody (mAb), that hasthe antigen-binding specificity of SEAM 3. In this embodiment, the SEAM3-reactive antigen may be present on the cell surface at any stage ofthe cell cycle, including during cell division. Of note is that in someinstances, cancers that present a SEAM 3-reactive antigen during celldivision may present a lower or no detectable level of SEAM 3-reactiveantigen when the cell is quiescent (i.e., not undergoing cell division).However, as illustrated in the examples below, SEAM 3-reactive antigencan be detected in non-dividing cells by detecting SEAM 3-reactiveantigen in a permeabilized test cell. A test cancer cell that exhibits apattern of staining with a SEAM 3 antibody (or an antibody having theantigen binding specificity of SEAM 3) that is distinct from a patternof antibody staining in a normal cell is identified as a cancerous cellthat exhibits a SEAM 3-reactive antigen. Such cancers are thus amenableto therapy with an antibody that specifically binds the SEAM 3-reactiveantigen (e.g., the mAb SEAM 3).

The above-described assay reagents, including the antibodies generatedby immunization with the deNAc SA antigen according to the methodsdescribed herein, can be provided in kits, with suitable instructionsand other necessary reagents, in order to conduct immunoassays asdescribed above. The kit can also contain, depending on the particularimmunoassay used, suitable labels and other packaged reagents andmaterials (i.e. wash buffers and the like). Standard immunoassays, suchas those described above, can be conducted using these kits.

Antibody-Based Therapies

Antibodies generated using the methods of the invention to treat orprevent cancer associated that presents a deNAc SA epitope in amammalian subject, particularly in a human. Antibodies generated using adeNAc SA antigen (including conjugates) can be provided in apharmaceutical composition suitable for administration to a subject, soas to provide for anti-cancer therapy.

More particularly, anti-deNAc SA epitope antibodies generated accordingto the methods described herein can be administered to a subject (e.g. ahuman patient) to, for example, facilitate reduction of viability ofcancerous cells, e.g., to provide for or enhance a immune response oranti-cancer therapy to reduce tumor size, reduce tumor load, and/orimprove the clinical outcome in patients. In particular, antibodies thathave the binding specificity of the mAb SEAM 3 (and thus bind theepitope bound by the mAb SEAM3) can be used to disrupt the cell cycle ofthe cancer cell, and facilitate entry of the cell into apoptosis, e.g.,by inducing cancerous cells to enter the pre-G_(o) cell cycle phase. Theantibodies can optionally have attached a an anti-cancer drug fordelivery to a site of a cancer cell to further facilitate tumor killingor clearance, e.g., an anti-proliferation moiety (e.g., VEGF antagonist,e.g., an anti-VEGF antibody), a toxin (e.g., an anti-cancer toxin, e.g.,ricin, Pseudomonas exotoxin A, and the like) , radionuclide (e.g. ⁹⁰Y,¹³¹I, ¹⁷⁷L and the like), anti-cancer drugs (e.g. doxorubicin,calicheamicin, maytansinoid DM1, auristatin caupecitabine,5-fluorouricil, leucovorin, irinotercan, and the like), and/or canoptionally be modified to provide for improved pharmacokinetic profile(e.g., by PEGylation, hyperglycosylation, and the like).

Methods for producing and formulating anti-deNAc SA epitope antibodiessuitable for administration to a subject (e.g., a human subject) arewell known in the art. For example, antibodies can be provided in apharmaceutical composition comprising an effective amount of an antibodyand a pharmaceutical excipients (e.g., saline). The pharmaceuticalcomposition may optionally include other additives (e.g., buffers,stabilizers, preservatives, and the like). An effective amount ofantibody is generally an amount effective to provide for enhancing ananti-cancer immune response in a subject for a desired period. Atherapeutic goal (e.g., reduction in tumor load) can be accomplished bysingle or multiple doses under varying dosing regimen.

Antibodies administered to an organism other than the species in whichthey are raised are often immunogenic. Thus, for example, murine orporcine antibodies administered to a human often induce an immunologicresponse against the antibody. The immunogenic properties of theantibody are reduced by altering portions, or all, of the antibody intocharacteristically human sequences thereby producing chimeric or humanantibodies, respectively.

Of particular interest are antibodies that have the antigen bindingspecificity of the mAb SEAM 3. Examples of such antibodies include thosehaving a light chain polypeptide comprising CDR1, CDR2 and CDR3 of thevariable reagion of a SEAM 3 light chain polypeptide (amino acidresidues 24 to 39, amino acid residues 55 to 61, and amino acid residues94 to 100, respectively set forth in FIG. 52) and a heavy chainpolypeptide comprising CDR1, CDR2, and CDR3 of the variable region ofthe SEAM 3 heavy chain polypeptide (amino acid residues amino acidresidues 26 to 35, amino acid residues 50 to 66, and amino acid residues101 to 108, respectively, set forth in FIG. 52). Such antibodies includechimeric antibodies, humanized antibodies, and the like.

Chimeric Antibodies

Chimeric antibodies are immunoglobulin molecules comprising a human andnon-human portion. More specifically, the antigen combining region (orvariable region) of a humanized chimeric antibody is derived from anon-human source (e.g. murine), and the constant region of the chimericantibody (which confers biological effector function to theimmunoglobulin) is derived from a human source. The chimeric antibodycan have the antigen binding specificity of the non-human antibodymolecule and the effector function conferred by the human antibodymolecule. A large number of methods of generating chimeric antibodiesare well known to those of skill in the art (see, e.g., U.S. Pat. Nos.5,502,167, 5,500,362, 5,491,088, 5,482,856, 5,472,693, 5,354,847,5,292,867, 5,231,026, 5,204,244, 5,202,238, 5,169,939, 5,081,235,5,075,431 and 4,975,369). An alternative approach is the generation ofhumanized antibodies by linking the CDR regions of non-human antibodiesto human constant regions by recombinant DNA techniques. See Queen etal., Proc. Natl. Acad. Sci. USA 86: 10029-10033 (1989) and WO 90/07861.

Recombinant DNA methods can be used to generate chimeric antibodies in arecombinant expression system. For example, a recombinant DNA vector isused to transfect a cell line that produces an anti-deNAc SA epitopeantibody. The recombinant DNA vector can contain a “replacement gene” toreplace all or a portion of the gene encoding the immunoglobulinconstant region in the cell line (e.g. a replacement gene may encode allor a portion of a constant region of a human immunoglobulin, or aspecific immunoglobulin class), and a “target sequence” which allows fortargeted homologous recombination with immunoglobulin sequences withinthe antibody producing cell (e.g., hybridoma).

In another example, a recombinant DNA vector is used to transfect a cellline that produces an antibody having a desired effector function (e.g.a constant region of a human immunoglobulin), in which case, thereplacement gene contained in the recombinant vector may encode all or aportion of a region of an antibody and the target sequence contained inthe recombinant vector allows for homologous recombination and targetedgene modification within the antibody producing cell. In eitherembodiment, when only a portion of the variable or constant region isreplaced, the resulting chimeric antibody may define the sameantigen-binding and/or have the same effector function yet be altered orimproved so that the chimeric antibody may demonstrate a greater antigenspecificity, greater affinity binding constant, increased effectorfunction, or increased secretion and production by the transfectedantibody producing cell line, etc.

Human Antibodies

In another embodiment, the anit-deNAc SA epitope antibodies are fullyhuman antibodies. Human antibodies are primarily composed ofcharacteristically human polypeptide sequences. The human antibodies ofthis invention can be produced by a wide variety of methods (see, e.g.,Larrick et al., U.S. Pat. No. 5,001,065). Human anti-deNAc SA epitopecan be produced initially in trioma cells (descended from three cells,two human and one mouse). Genes encoding the antibodies are then clonedand expressed in other cells, particularly non-human mammalian cells.The general approach for producing human antibodies by trioma technologyhas been described by Ostberg et al. (1983), Hybridoma 2: 361-367,Ostberg, U.S. Pat. No. 4,634,664, and Engelman et al., U.S. Pat. No.4,634,666. Triomas have been found to produce antibody more stably thanordinary hybridomas made from human cells.

Cancer Therapy

Antibodies that specifically bind a deNAc SA epitope can be used inanti-cancer therapy for a mammalian subject, particularly a human, wherethe cancerous cells present a deNAc SA epitope on an extracellularlyaccessible cell surface (e.g., a deNAc SA epitope on an at leastpartially de-N-acetylated ganglioside). Particularly, the antibodiesgenerated using the deNAc SA antigens (including deNAc SA antigenconjugates) can be provided in a pharmaceutical composition suitable foradministration to a subject in need of treatment.

Therapeutic administration of the subject antibodies can includeadministration as a part of a therapeutic regimen that may or may not bein conjunction with additional standard anti-cancer therapeutics,including but not limited to chemotherapeutic agents and surgery (e.g.,as those described further below). In addition, therapeuticadministration of the subject antibodies can also be post-therapeutictreatment of the subject with an anti-cancer therapy, where theanti-cancer therapy can be, for example, surgery, radiation therapy,administration of chemotherapeutic agents, and the like. Use ofmonoclonal antibodies, particularly monoclonal antibodies that canprovide for complement-mediated killing, and/or antibody-dependentcellular cytotoxicity-mediated killing, of a target cell are ofparticular interest.

In certain embodiments, the antibody can be provided alone or can beoptionally attached to a compound to facilitate delivery of the compoundto the cancer cell to facilitae tumor killing or clearance, e.g., atoxin (e.g., ricin, diptheria toxin, Pseudomonas exotoxin A or othertoxin), a radionuclide or other molecule that is cytotoxic (⁹⁰Y, ¹³¹I,¹⁷⁷L and the like). The antibody (or, where bound to a compound, theantibody-compound conjugate) can be provided in solution (e.g., dilutedin normal saline solution, PBS, or normal saline or PBS in combinationwith human albumin (5%)). The antibody can be provided at concentrationranging from about 0.1 mg/ml to about 10 mg/ml, including from about 0.5mg/ml to about 9 mg/ml, about 1 mg/ml to about 8 mg/ml, about 1.5 mg/mlto about 7.5 mg/ml, about 2 mg/ml to about 7 mg/ml, about 2.5 mg/ml toabout 6.5 mg/ml, about 3 mg/ml to about 6 mg/ml, about 3.5 mg/ml toabout 5.5 mg/ml, about 4 mg/ml to about 5 mg/ml, and the like.

In other embodiments, the antibody can be adminsitered in combinationwith one or more chemotherapeutic agents (e.g., cyclophosphamide,doxorubicin, vincristine and prednisone (CHOP)), and/or in combinationwith radiation treatment and/or in combination with surgicalintervention (e.g., pre- or post-surgery to remove a tumor). Where theanti-deNAc SA epitope antibody is used in connection with surgicalintervention, the antibody can be administered prior to, at the time of,or after surgery to remove cancerous cells, and may be administeredsystemically or locally at the surgical site. . The antibody alone or incombinations described above can be administered systemically (e.g., byparenteral administration, e.g., by an intravenous route) or locally(e.g., at a local tumor site, e.g., by intratumoral administration(e.g., into a solid tumor, into an involved lymph node in a lymphoma orleukemia), administration into a blood vessel supplying a solid tumor,etc.). Antibody administration by can be accomplished by infusion, e.g.,by infusion at a rate of about 50 mg/h to about 400 mg/h, includingabout 75 mg/h to about 375 mg/h, about 100 mg/h to about 350 mg/h, about150 mg/h to about 350 mg/h, about 200 mg/h to about 300 mg/h, about 225mg/h to about 275 mg/h. Exemplary rates of infusion can achieve adesired therapeutic dose of, for example, about 0.5 mg/m²/day to about10 mg/m²/day, including about 1 mg/m²/day to about 9 mg/m²/day, about 2mg/m²/day to about 8 mg/m²/day, about 3 mg/m²/day to about 7 mg/m²/day,about 4 mg/m²/day to about 6 mg/m²/day, about 4.5 mg/m²/day to about 5.5mg/m²/day. Administration (e.g, by infusion) can be repeated over adesired period, e.g., repeated over a period of about 1 day to about 5days or once every several days, for example, about five days, overabout 1 month, about 2 months, etc.

Antibody-Based Therapy of Metastases

A primary problem with treating cancer is metastases or the propensityfor being released from the primary site of the tumor, traveling in theblood stream to distal sites, followed by attachment to tissues atdistal sites and secondary tumor formation. The problem is oftenexacerbated during surgical removal of the primary tumor as the resultof mechanical disruption of the mass results in metastasis and adhesionto a secondary location following surgery. Treatment with an anti-deNAcSA epitope antibody (e.g., SEAM 3) after identification of a primarytumor composed of cells expressing a deNAc SA epitope (e.g., ade-N-acetyl ganglioside) and/or after surgical removal of a tumor canprevent adhesion of the any cancer cells following metastasis, and iscontemplated by the invention. In addition, anti-deNAc SA epitopeantibody (e.g., SEAM 3) binding to cancer cells that express a deNAc SAepitope (e.g., de-N-acetyl ganglioside or sialic acid modified protein)can provide for a cytotoxic effect on cells that is independent ofcomplement (see Examples Section). Therefore, in certain embodiments, ananti-deNAc SA epitope antibody (e.g., SEAM 3) is useful in treatingcancer patients who have a complement deficiency, e.g., as a result of aenvironmental exposure (e.g, a drug therapy), a genetic deficiency, etc.Examples of complement deficiences include those involving inhibition ofC1, C2, C6, C9, and properdin.

Combination Cancer Therapies

Any of a wide variety of cancer therapies can be used in combinationwith the deNAc SA-based or anti-deNAc SA epitope antibody-basedtherapies described herein. Such cancer therapies include surgery (e.g.,surgical removal of cancerous tissue), radiation therapy, bone marrowtransplantation, chemotherapeutic treatment, biological responsemodifier treatment, and certain combinations of the foregoing.

Radiation therapy includes, but is not limited to, X-rays or gamma raysthat are delivered from either an externally applied source such as abeam, or by implantation of small radioactive sources.

Chemotherapeutic agents are non-peptidic (i.e., non-proteinaceous)compounds that reduce proliferation of cancer cells, and encompasscytotoxic agents and cytostatic agents. Non-limiting examples ofchemotherapeutic agents include alkylating agents, nitrosoureas,antimetabolites, antitumor antibiotics, plant (vinca) alkaloids, andsteroid hormones.

Agents that act to reduce cellular proliferation are known in the artand widely used. Such agents include alkylating agents, such as nitrogenmustards, nitrosoureas, ethylenimine derivatives, alkyl sulfonates, andtriazenes, including, but not limited to, mechlorethamine,cyclophosphamide (CYTOXAN™), melphalan (L-sarcolysin), carmustine(BCNU), lomustine (CCNU), semustine (methyl-CCNU), streptozocin,chlorozotocin, uracil mustard, chlormethine, ifosfamide, chlorambucil,pipobroman, triethylenemelamine, triethylenethiophosphoramine, busulfan,dacarbazine, and temozolomide.

Antimetabolite agents include folic acid analogs, pyrimidine analogs,purine analogs, and adenosine deaminase inhibitors, including, but notlimited to, cytarabine (CYTOSAR-U), cytosine arabinoside, fluorouracil(5-FU), floxuridine (FudR), 6-thioguanine, 6-mercaptopurine (6-MP),pentostatin, 5-fluorouracil (5-FU), methotrexate,10-propargyl-5,8-dideazafolate (PDDF, CB3717),5,8-dideazatetrahydrofolic acid (DDATHF), leucovorin, fludarabinephosphate, pentostatine, and gemcitabine.

Suitable natural products and their derivatives, (e.g., vinca alkaloids,antitumor antibiotics, enzymes, lymphokines, and epipodophyllotoxins),include, but are not limited to, Ara-C, paclitaxel (TAXOL®), docetaxel(TAXOTERE®), deoxycoformycin, mitomycin-C, L-asparaginase, azathioprine;brequinar; alkaloids, e.g. vincristine, vinblastine, vinorelbine,vindesine, etc.; podophyllotoxins, e.g. etoposide, teniposide, etc.;antibiotics, e.g. anthracycline, daunorubicin hydrochloride (daunomycin,rubidomycin, cerubidine), idarubicin, doxorubicin, epirubicin andmorpholino derivatives, etc.; phenoxizone biscyclopeptides, e.g.dactinomycin; basic glycopeptides, e.g. bleomycin; anthraquinoneglycosides, e.g. plicamycin (mithramycin); anthracenediones, e.g.mitoxantrone; azirinopyrrolo indolediones, e.g. mitomycin; macrocyclicimmunosuppressants, e.g. cyclosporine, FK-506 (tacrolimus, prograf),rapamycin, etc.; and the like.

Other anti-proliferative cytotoxic agents are navelbene, CPT-11,anastrazole, letrazole, capecitabine, reloxafine, cyclophosphamide,ifosamide, and droloxafine.

Microtubule affecting agents that have antiproliferative activity arealso suitable for use and include, but are not limited to,allocolchicine (NSC 406042), Halichondrin B (NSC 609395), colchicine(NSC 757), colchicine derivatives (e.g., NSC 33410), dolstatin 10 (NSC376128), maytansine (NSC 153858), rhizoxin (NSC 332598), paclitaxel(TAXOL®), TAXOL® derivatives, docetaxel (TAXOTERE®), thiocolchicine (NSC361792), trityl cysterin, vinblastine sulfate, vincristine sulfate,natural and synthetic epothilones including but not limited to,eopthilone A, epothilone B, discodermolide; estramustine, nocodazole,and the like.

Hormone modulators and steroids (including synthetic analogs) that aresuitable for use include, but are not limited to, adrenocorticosteroids,e.g. prednisone, dexamethasone, etc.; estrogens and pregestins, e.g.hydroxyprogesterone caproate, medroxyprogesterone acetate, megestrolacetate, estradiol, clomiphene, tamoxifen; etc.; and adrenocorticalsuppressants, e.g. aminoglutethimide; 17α-ethinylestradiol;diethylstilbestrol, testosterone, fluoxymesterone, dromostanolonepropionate, testolactone, methylprednisolone, methyl-testosterone,prednisolone, triamcinolone, chlorotrianisene, hydroxyprogesterone,aminoglutethimide, estramustine, medroxyprogesterone acetate,leuprolide, Flutamide (Drogenil), Toremifene (Fareston), and ZOLADEX®.Estrogens stimulate proliferation and differentiation, thereforecompounds that bind to the estrogen receptor are used to block thisactivity. Corticosteroids may inhibit T cell proliferation.

Other chemotherapeutic agents include metal complexes, e.g. cisplatin(cis-DDP), carboplatin, etc.; ureas, e.g. hydroxyurea; and hydrazines,e.g. N-methylhydrazine; epidophyllotoxin; a topoisomerase inhibitor;procarbazine; mitoxantrone; leucovorin; tegafur; etc. Otheranti-proliferative agents of interest include immunosuppressants, e.g.mycophenolic acid, thalidomide, desoxyspergualin, azasporine,leflunomide, mizoribine, azaspirane (SKF 105685); IRESSA® (ZD 1839,4-(3-chloro-4-fluorophenylamino)-7-methoxy-6-(3-(4-morpholinyl)propoxy)quinazoline);etc.

“Taxanes” include paclitaxel, as well as any active taxane derivative orpro-drug. “Paclitaxel” (which should be understood herein to includeanalogues, formulations, and derivatives such as, for example,docetaxel, TAXOL™, TAXOTERE™ (a formulation of docetaxel), 10-desacetylanalogs of paclitaxel and 3′N-desbenzoyl-3′N-t-butoxycarbonyl analogs ofpaclitaxel) may be readily prepared utilizing techniques known to thoseskilled in the art (see also WO 94/07882, WO 94/07881, WO 94/07880, WO94/07876, WO 93/23555, WO 93/10076; U.S. Pat. Nos. 5,294,637; 5,283,253;5,279,949; 5,274,137; 5,202,448; 5,200,534; 5,229,529; and EP 590,267),or obtained from a variety of commercial sources, including for example,Sigma Chemical Co., St. Louis, Mo. (T7402 from Taxus brevifolia; orT-1912 from Taxus yannanensis).

Paclitaxel should be understood to refer to not only the commonchemically available form of paclitaxel, but analogs and derivatives(e.g., TAXOTERE™ docetaxel, as noted above) and paclitaxel conjugates(e.g., paclitaxel-PEG, paclitaxel-dextran, or paclitaxel-xylose).

Also included within the term “taxane” are a variety of knownderivatives, including both hydrophilic derivatives, and hydrophobicderivatives. Taxane derivatives include, but not limited to, galactoseand mannose derivatives described in International Patent ApplicationNo. WO 99/18113; piperazino and other derivatives described in WO99/14209; taxane derivatives described in WO 99/09021, WO 98/22451, andU.S. Pat. No. 5,869,680; 6-thio derivatives described in WO 98/28288;sulfenamide derivatives described in U.S. Pat. No. 5,821,263; and taxolderivative described in U.S. Pat. No. 5,415,869. It further includesprodrugs of paclitaxel including, but not limited to, those described inWO 98/58927; WO 98/13059; and U.S. Pat. No. 5,824,701.

Cancers Amenable to Therapy by deNAC SA Antigen Immunization-Based OrAntibody-Based Therapy

The deNAc SA antigen find use in a variety of cancer therapies(including cancer prevention (e.g., cancer vaccine) and post-diagnosiscancer therapy) or cancer diagnostics for cancers having a cell surfacedeNAc SA epitope. Subjects having, suspected of having or at risk ofdeveloping a tumor are contemplated for therapy and diagnosis describedherein. Samples obtained from such subject are likewise suitable for usein the methods of the invention.

Cancers having a cell surface-accessible deNAc SA epitope include thosehaving an at least partially de-N-acetylated ganglioside and/or aprotein having a sialic acid modification that contains a deNAc SAepitope. Cancers having de-N-acetylated gangliosides have beendescribed.

The presence of de-N-acetyl sialic acid residues in normal human tissueappears to be transient and very low abundance, being found only in afew blood vessels, infiltrating mononuclear cells in the skin and colon,and at moderate levels in skin melanocytes. It is prevalent only inabnormal cells, such as melanomas, leukemias and lymphomas. Sinceexpression of high levels of deNAc SA antigens (e.g., de-N-acetylgangliosides) occurs predominantly in cancer cells, immunization withdeNAc SA antigens can be used to elicit antibodies that can affectcomplement-mediated cytotoxicity and antibody-dependent cellularcytotoxicity, and can block tumor growth. In addition, antibodies thatare specific for short de-N-acetyl sialic acid oligomers found in somegangliosides can be used therapeutically to effect complement-mediatedcytotoxicity and antibody-dependent cellular cytotoxicity, and can blocktumor growth and prevent adhesion and invasion of cancer cells in othertissues.

Exemplary cancers presenting a deNAc SA epitope include cancer cellspresenting a de-N-acetyl ganglioside containing a de-N-acetyl sialicacid residue (e.g. GM2alpha, GM1alpha, GD1beta, GM1b, GD1c, GD1alpha,GM3, GM2, GM1, GD13, GT13, GT1halpha, GD3, GD2, GD1b, GT1b, GQ1b,Gomega1halpha, GT3, GT2, GT1c, GQ1c, and GP1c). Of particular interestare gangliosides that contain two or more sialic acid residues linked byalpha 2-8 glycosidic bonds (e.g., GD1c, GT13, GD3, GD1b, GT1b, GQ1b,Gomegalhalpha, GT3, GT1c, GQ1c, and GP1c) in which at least one residueis de-N-acetylated. In some embodiments, the ganglioside that containstwo or more sialic acid residues linked by alpha 2-8 glycosidic bonds isa ganglioside other than GD3 and/or other than GM3. In some embodiments,the target of the cancer is a deNAc SA epitope other than one present ona de-N-acetylated ganglioside (e.g., a de-N-acetylated residue of asialic acid-modified protein).

In one embodiment antibodies that specifically bind a SEAM 3 reactiveantigen are used in treatment oc cancers that present a SEAM 3 reactiveantigen on an cell surface, including cancers that exhibit anextracellularlly accessible SEAM 3-reactive antigen during celldivision. Cancers that present a SEAM 3-reactive antigen, particularly acell surface SEAM 3-reactive antigen, are particularly amenable totherapy with an antibody having the antigen binding specifity of themonoclonal antibody SEAM 3, including cancers that exhibit anextracellularlly accessible SEAM 3-reactive antigen during celldivision.

It should be noted that deNAc SA epitopes and/or SEAM 3-reactiveantigens against which cancer therapy is directed may be expressed athigher levels on a cancer cell compared to a non-cancerous cell so as tomitigate damage to normal cells, this is not a limitation of thetherapies disclosed herein. For example, where the cancer involves acell type that can be replenished (e.g., B cell, T cell, or other cellof hematopoietic origin, as in leukemias and lymphomas), binding ofanti-deNAc SA epitope antibodies (e.g., SEAM 3) to normal cells can beacceptable since damage to a subject by depleting such cells can betreated (e.g., with drugs to stimulate repopulation of normal cells,e.g., GM-CSF, EPO, and the like).

The methods relating to cancer contemplated herein include, for example,use of deNAc SA antigens as a anti-cancer vaccine or therapy, as well asuse of antibodies generated using deNAc SA antigens in anti-cancervaccines (e.g., by passive immunization) or therapies. The methods areuseful in the context of treating or preventing a wide variety ofcancers, including carcinomas, sarcomas, leukemias, and lymphomas.

Carcinomas that can be amenable to therapy by a method disclosed hereininclude, but are not limited to, esophageal carcinoma, hepatocellularcarcinoma, basal cell carcinoma (a form of skin cancer), squamous cellcarcinoma (various tissues), bladder carcinoma, including transitionalcell carcinoma (a malignant neoplasm of the bladder), bronchogeniccarcinoma, colon carcinoma, colorectal carcinoma, gastric carcinoma,lung carcinoma, including small cell carcinoma and non-small cellcarcinoma of the lung, adrenocortical carcinoma, thyroid carcinoma,pancreatic carcinoma, breast carcinoma, ovarian carcinoma, prostatecarcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous glandcarcinoma, papillary carcinoma, papillary adenocarcinoma,cystadenocarcinoma, medullary carcinoma, renal cell carcinoma, ductalcarcinoma in situ or bile duct carcinoma, choriocarcinoma, seminoma,embryonal carcinoma, Wilm's tumor, cervical carcinoma, uterinecarcinoma, testicular carcinoma, osteogenic carcinoma, epitheliealcarcinoma, and nasopharyngeal carcinoma.

Sarcomas that can be amenable to therapy by a method disclosed hereininclude, but are not limited to, fibrosarcoma, myxosarcoma, liposarcoma,chondrosarcoma, chordoma, osteogenic sarcoma, osteosarcoma,angiosarcoma, endotheliosarcoma, lymphangiosarcoma,lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's sarcoma,leiomyosarcoma, rhabdomyosarcoma, and other soft tissue sarcomas.

Other solid tumors that can be amenable to therapy by a method disclosedherein include, but are not limited to, glioma, astrocytoma,medulloblastoma, craniopharyngioma, ependymoma, pinealoma,hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma,melanoma, neuroblastoma, and retinoblastoma.

Leukemias that can be amenable to therapy by a method disclosed hereininclude, but are not limited to, a) chronic myeloproliferative syndromes(neoplastic disorders of multipotential hematopoietic stem cells); b)acute myelogenous leukemias (neoplastic transformation of amultipotential hematopoietic stem cell or a hematopoietic cell ofrestricted lineage potential; c) chronic lymphocytic leukemias (CLL;clonal proliferation of immunologically immature and functionallyincompetent small lymphocytes), including B-cell CLL, T-cell CLLprolymphocytic leukemia, and hairy cell leukemia; and d) acutelymphoblastic leukemias (characterized by accumulation of lymphoblasts).Lymphomas that can be treated using a subject method include, but arenot limited to, B-cell lymphomas (e.g., Burkitt's lymphoma); Hodgkin'slymphoma; non-Hodgkin's lymphoma, and the like.

Other cancers that can be amenable to treatment according to the methodsdisclosed herein include atypical meningioma (brain), islet cellcarcinoma (pancreas), medullary carcinoma (thyroid), mesenchymoma(intestine), hepatocellular carcinoma (liver), hepatoblastoma (liver),clear cell carcinoma (kidney), and neurofibroma mediastinum.

Further exemplary cancers that can be amenable to treatment using amethods disclosed herein include, but art not limited to, cancers ofneuroectodermal and epithelial origin. Examples of cancers ofneuroectodermal origin include, but are not limited to, Ewings sarcoma,spinal tumors, brain tumors, supratenbrial primative neuroectodermaltumors of infancy, tubulocystic carcinoma, mucinous tubular and spindlecell carcinoma, renal tumors, mediastinum tumors, neurogliomas,neuroblastomas, and sarcomas in adolescents and young adults. Examplesof epithelial origin include, but are not limited to, small cell lungcancer, cancers of the breast, eye lens, colon, pancreas, kidney, liver,ovary, and bronchial epithelium. In some embodiments, the subjectmethods do not include treatment of melanoma (i.e., the cancer is otherthan melanoma). In other embodiments, the subject methods do not includetreatment of lymphoma (i.e., the cancer is other than lymphoma).

In certain embodiments, the methods of the present invention are used totreat cancer cells known to express de-N-acetyl gangliosides includemelanomas and some lymphomas. Cancers that overexpress the precursorgangliosides GM3 and GD3 are likely to also express the greatest amountof de-N-acetyl gangliosides on the cell surface.

In one embodiment, the cancer is one that presents a SEAM 3-reactiveantigen. Cancers that present a SEAM 3-reactive antigen can beidentified by methods known in the art. Exemplary methods of detectionand diagnosis are described below.

Where the anti-cancer therapy comprises administration of an antibodythat having the antigen-binding specificity of the monoclonal antibody(mAb) SEAM 3 (discussed below in detail), the anti-cancer therapy can beparticularly directed to dividing (replicating, proliferating) cancerouscells. As shown in the Examples below, the epitope specifically bound bySEAM 3 is primarily accessible during cell division. That is, the levelof extracellularly accessible antigen bound by SEAM3 is increased duringcell division as compared to non-dividing cells, and binding of SEAM3drives the cell toward anaphase (into pre-G₀). Since most cancers aremore rapidly dividing that normal cells of the same type, antibodiesthat bind a SEAM 3-reactive antigen are attractive for antibody-basedcancer therapy.

Thus the present disclosure particularly provides anti-cancer therapydirected toward cancerous cells involving administration of an antibodyhaving the antigen binding specificity of the SEAM 3 mAb. Cancersparticularly amenable to antibody therapy using an antibody having theantigen binding specificity of SEAM 3 can be identified by examiningmarkers of cellular proliferation (e.g., Ki-67 antigen) and/or byexamining the accessibility of the deNAc SA epitope bound by SEAM 3 individing cells (e.g., as in an in vitro assay).

Antibodies Having Antigen Binding Specificty of Seam 3 MonoclonalAntibod

The disclosure provides recombinant monoclonal antibodies (mAbs), andnucleic acid encoding such antibodies, wherein the recombinant mAbs havethe antigen specificity of SEAM3, which MAb binds to de-N-acetylatedgangliosides on the surface of cancer cells, and facilitates reductionof cell viability of cancer cells. Recombinant antibodies having theantigen binding specificity of SEAM3 include antibodies having at leastan antigen binding portion of SEAM3. Such recombinant mAbs can bedescribed as having the following general characteristics:

a) high affinity for a deNAc SA epitope, particularly a deNAc SA epitopeon an extracellullary accessible surface of a cancerous cell (e.g., aK_(d) of about 10⁻⁶, about 10⁻⁸ or less;

b) slow off rate for dissociation with a deNAc SA antigen (e.g., aK_(off) of about 1×10⁻³ sec⁻¹or less);

c) does not significantly bind to polysialic acid that does not containde-N-acetyl residues;

d) activity in facilitating loss of adherence of cancerous cells havinga cell surface deNAc SA epitope (e.g., a de-N-acetylated ganglioside) invitro;and

e) activity in facilitating reduction of viability of a cancerous cellhaving cell surface deNAc SA epitope or particularly SEAM 3-reactiveantigen, which antibody may disrupt the cell cycle and/or be capable ofbinding complement and/or direct ADCC against the cancer cell to whichit is bound.

Antibodies having the antigen binding specificity of SEAM 3 can beproduced by immunization-based techniques, and screening for antibodiesthat competitively bind SEAM 3 reactive antigen. Such antibodies canalso be generated by recombinant methods, using the information providedby the amino acid and encoding polynucleotides of the SEAM 3 mAb heavychain polypeptide and light chain polypeptide disclosed herein. Forexample, antibodies having the antigen binding specificity of SEAM 3 canbe generated by producing a recombinant light chain polypeptidecomprising CDR1, CDR2 and CDR3 of the variable reagion of a SEAM 3 lightchain polypeptide (contiguous amino acid residues 24 to 39, continguousamino acid residues 55 to 61, and contiguous amino acid residues 94 to100, respectively set forth in FIG. 52) and producing a heavy chainpolypeptide comprising CDR1, CDR2, and CDR3 of the variable region ofthe SEAM 3 heavy chain polypeptide (contiguous amino acid residues 26 to35, contiguous amino acid residues 50 to 66, and contiguous amino acidresidues 101 to 108, respectively, set forth in FIG. 52). Theses CDRscan be provided in a light chain polypeptide and heavy chainpolypeptide, respectcively, flanked by appropriate framework residues toprovide for formation of an antigen binding site having the antigenbinding specificity of SEAM 3. Such antibodies can take any of a varietyof forms, including F(ab) fragments, single chain antibodies, chimericantibodies, humanized antibodies, and the like.

Methods for measuring binding affinity, off rate and other antibodybinding kinetics are well known in the art, and may be employed todetermine whether an antibody has a high affinity and a slow off ratefor a deNAc SA antigen. In many methods and as is well known in the art,antibody binding kinetics may be measured by ELISA methods or bymeasuring surface plasmon resonance using, for example, a BIACORE™biosensor (Pharmacia/Pfizer) or differential scanning calorimetry(Bliznukov et al. 2001 Biochemistry (Mosc) 66:27-33). Methods formeasuring binding of antigens to antibodies using surface plasmonresonance are well known in the art (see, e.g., Methods of Dev. Biol.2003 112:141-51 and J. Mol. Recognit. 1999 12:310-5) and are readilyadapted for use herein.

In certain embodiments a recombinant monoclonal antibody having aantigen-binding characteristics of SEAM3 MAb has a heavy chain having anamino acid sequence that is substantially identical (e.g., at leastabout 70%, at least about 80%, at least about 90%, at least about 95% orat least about 98% identical) to that of a contiguous sequence of theSEAM3 heavy chain variable domain, and a light chain that issubstantially identical (e.g., at least about 70%, at least about 80%,at least about 90%, at least about 95% or at least about 98% identical)to a contiguous sequence of the SEAM3 light chain variable domain. Inparticular embodiments, a recombinant antibody has framework or CDRamino acid sequences that are substantially identical (e.g., at leastabout 70%, at least about 80%, at least about 90%, at least about 95% orat least about 98% identical) to a contiguous framework sequence or acontiguous CDR sequence of any of the heavy or light chain sequencesshown in FIGS. 46 and 47. Such polypeptides are useful in constructingchimeric antibodies having antigen-binding specificity of SEAM 3. Suchcontiguous sequences can include the CDRs of the light chainpolypeptides (L-CDR1, L-CDR2, L-CDR3) and/or heavy chain polypeptides(H—CDR1, H—CDR2, H—CDR3).

In certain embodiments, recombinant monoclonal antibodies contain aheavy or light chain that is encoded by a polynucleotide that hybridizesunder high stringency conditions to a SEAM3 heavy or lightchain-encoding nucleic acid. High stringency conditions includeincubation at 50° C. or higher in 0.1×SSC (15 mM saline/0.15 mM sodiumcitrate). Such polynucleotides are useful in detection of SEAM 3antibody production in a cell, as well as in constructing chimericantibodies having antigen-binding specificity of SEAM 3.

In certain embodiments, recombinant monoclonal antibodies of theinvention may contain a heavy or light chain that is encoded by apolynucleotide having a nucleotide sequence that is at least 80%identical to (e.g., at least 85%, at least 90%, at least 95%, at least98%) to a contiguous sequence of a SEAM3 heavy or light chain-encodingnucleic acid. The percentage identity is based on the shorter of thesequences compared. Well known programs such as BLASTN (2.0.8) (Altschulet al. (1997) Nucl. Acids. Res. 25:3389-3402) using default parametersand no filter may be employed to make a sequence comparison.

The recombinant monoclonal antibody may be a full-length antibody or anychimera thereof, for example. Methods for producing chimeric antibodiesare known in the art. See e.g., Morrison et al (Science 1985 229:1202);Oi et al (BioTechniques 1986 4:214); Gillies et al. (J. Immunol. Methods1989 125:191-202) and U.S. Pat. Nos. 5,807,715, 4,816,567 and 4,816397,which are incorporated herein by reference in their entirety.

The amino acid sequences of the CDRs of the heavy and light chains ofSEAM3 are provided in FIGS. 52 and framework and CDR regions are definedin FIGS. 53 and 54, for SEAM3 light and heavy chains respectively.

The disclosure also provides antibodies that are modified by conjugationto a moiety that can provide for a desired characteristic (e.g.,increase in serum half-life, anti-cancer activity, etc.). Such antibodyconjugates are exemplified below.

Modified Antibodies Having Antigen Binding Specificity of SEAM3

The above-described recombinant monoclonal antibodies having an antigenbinding region of SEAM3 may be modified to provide modified antibodiesthat bind a deNAc SA epitope, and have a desired activity, e.g.,enhanced ability to facilitate reduction of cancer cell viability,enhanced serum half-life, reduced immunogenicity, and the like. Themodified antibodies may be made by substituting, adding, or deleting atleast one amino acid of an above-described SEAM3 monoclonal antibody. Inone embodiment, the SEAM3 antibody is modified to provide a humanizedantibody for human therapeutic use, or another type of modifiedantibody. In general, these modified antibodies have the generalantigen-binding characteristics of the SEAM3 antibody, and contain atleast the CDRs of a SEAM3 antibody heavy chain polypeptide and a SEAM3light chain polypeptide.

Guidance for amino acid substitutions that may be made can be found inthe accompanying FIGS. 52, 53 and 54 which illustrate the sequences andpositions of the CDRs in the heavy and light chain polypeptides andencoding DNA sequences of SEAM3. For example, in some embodiments,variants can be generated by making amino acid changes (e.g,.substitutions, particularly conservative amino acid substitutions) inthe areas outside the CDRs so identified. Further guidance for aminoacid substitutions can be found by aligning the amino acid sequences ofother anti-deNAc SA epitope antibodies with that of SEAM3, and notingregions that are conserved or variable, and making changes in thevariable regions that lie outside the CDRs.

In particular embodiments, these methods include making one or moreamino acid substitutions (e.g., one, up to two, up to three, up to fouror up to five of more, usually up to 10 or more). An amino acidsubstitution may be at any position, and the amino acid at that positionmay be substituted by an amino acid of any identity. Preferably, amodified antibody has the same general characteristics of the SEAM3 MAb.In one embodiment, after a substitutable position has been identified byalignment of the sequences provided herein with the sequences of otherantibodies, the amino acids at that position may be substituted. Inparticular embodiments, an amino acid substitution may be a humanizingsubstitution (i.e., a substitution that make the amino acid sequencemore similar to that of a human antibody), a directed substitution(e.g., a substitution that make the amino acid sequence of an antibodymore similar to that of a related antibody in the same group), a randomsubstitution (e.g., a substitution with any of the 20naturally-occurring amino acids) or a conservative substitution (e.g., asubstitution with an amino acid having biochemical properties similar tothat being substituted).

In certain embodiments, modified antibodies of the invention may containa heavy or light chain that is encoded by a polynucleotide thathybridizes under high stringency conditions to a SEAM3 heavy or lightchain-encoding nucleic acid, particularly to the fragments encodingCDR1, CDR2 and CDR3 of the variable region of a SEAM 3 light chainpolypeptide (contiguous amino acid residues 24 to 39, continguous aminoacid residues 55 to 61, and contiguous amino acid residues 94 to 100,respectively set forth in FIG. 52) and to fragments encoding CDR1, CDR2,and CDR3 of the variable region of the SEAM 3 heavy chain polypeptide(contiguous amino acid residues 26 to 35, contiguous amino acid residues50 to 66, and contiguous amino acid residues 101 to 108, respectively,set forth in FIG. 52).. High stringency conditions include incubation at50° C. or higher in 0.1×SSC (15 mM saline/0.15 mM sodium citrate).

In certain embodiments, modified antibodies of the invention may containa heavy or light chain that is encoded by a polynucleotide that is atleast 80% identical to (e.g., at least 85%, at least 90%, at least 95%,at least 98%) the contiguous SEAM3 heavy or light chain-encoding nucleicacid. The percentage identity is based on the shorter of the sequencescompared. Well known programs such as BLASTN (2.0.8) (Altschul et al.(1997) Nucl. Acids. Res. 25:3389-3402) using default parameters and nofilter may be employed to make a sequence comparison.

Humanized Antibodies

In one embodiment, the invention provides humanized versions of theSEAM3 monoclonal antibody. In general, humanized antibodies can be madeby substituting amino acids in the framework regions of a parentnon-human antibody to produce a modified antibody that is lessimmunogenic in a human than the parent non-human antibody. Antibodiescan be humanized using a variety of techniques known in the artincluding, for example, CDR-grafting (EP 239,400; PCT publication WO91/09967; U.S. Pat. Nos. 5,225,539; 5,530,101; and 5,585,089), veneeringor resurfacing (EP 592,106; EP 519,596; Padlan, Molecular Immunology28(4/5):489-498 (1991); Studnicka et al., Protein Engineering7(6):805-814 (1994); Roguska. et al., PNAS 91:969-973 (1994)), and chainshuffling (U.S. Pat. No. 5,565,332). In certain embodiments, frameworksubstitutions are identified by modeling of the interactions of the CDRand framework residues to identify framework residues important forantigen binding and sequence comparison to identify unusual frameworkresidues at particular positions (see, e.g., U.S. Pat. No. 5,585,089;Riechmann et al., Nature 332:323 (1988)). Additional methods forhumanizing antibodies contemplated for use in the present invention aredescribed in U.S. Pat. Nos. 5,750,078; 5,502,167; 5,705,154; 5,770,403;5,698,417; 5,693,493; 5,558,864; 4,935,496; and 4,816,567, and PCTpublications WO 98/45331 and WO 98/45332. In particular embodiments, theSEAM3 antibody may be humanized according to the methods set forth inpublished U.S. published patent application nos. 20040086979 and20050033031. Accordingly, the SEAM3 antibody described above may behumanized using methods that are well known in the art.

A humanized SEAM3 antibody therefore may contain the unaltered CDRs ofthe SEAM3 antibody, or, in certain embodiments, altered CDRs of theSEAM3 antibody. A humanized antibody containing altered CDRs of theSEAM3 antibody generally contains CDRs having 1, up to 2, up to 3, up to4, up to 5, up to 6, up to 7 and in certain cases up to about 10 aminoacid substitutions, as compared to the CDRs of the SEAM3 antibody. Theparticular substitutable positions of a CDR, as well as the donor aminoacid that can be substituted into those positions, can be determined byalignment of the nucleic acid and/or amino acid sequences of SEAM3provided herein with that of other antibodies.

Polyethylene Glycol (PEG)-Modified Antibodies

Anti-deNAc SA epitope antibodies contemplated herein include PEGylatedanti-deNAc SA epitope antibodies, with PEGylated recombinant anti-deNAcSA epitope antibodies having antigen specificity of SEAM3 being ofparticular interest. Methods and reagents suitable for PEGylation of anantibody are well known in the art. In general, PEG suitable forconjugation to an antibody is generally soluble in water at roomtemperature, and has the general formula R(O—CH₂—CH₂)_(n)O—R, where R ishydrogen or a protective group such as an alkyl or an alkanol group, andwhere n is an integer from 1 to 1000. Where R is a protective group, itgenerally has from 1 to 8 carbons.

In many embodiments, PEG has at least one hydroxyl group, e.g., aterminal hydroxyl group, which hydroxyl group is modified to generate afunctional group that is reactive with an amino group, e.g., an epsilonamino group of a lysine residue, a free amino group at the N-terminus ofa polypeptide, or any other amino group such as an amino group ofasparagine, glutamine, arginine, or histidine.

In other embodiments, PEG is derivatized so that it is reactive withfree carboxyl groups in the antibody polypeptide, e.g., the freecarboxyl group at the carboxyl terminus of the antibody polypeptide.Suitable derivatives of PEG that are reactive with the free carboxylgroup at the carboxyl-terminus of a heavy chain or light chainpolypeptide include, but are not limited to PEG-amine, and hydrazinederivatives of PEG (e.g., PEG-NH—NH₂).

In other embodiments, PEG is derivatized such that it comprises aterminal thiocarboxylic acid group, —COSH, which selectively reacts withamino groups to generate amide derivatives. Because of the reactivenature of the thio acid, selectivity of certain amino groups over othersis achieved. For example, —SH exhibits sufficient leaving group abilityin reaction with N-terminal amino group at appropriate pH conditionssuch that the ϵ-amino groups in lysine residues are protonated andremain non-nucleophilic. On the other hand, reactions under suitable pHconditions may make some of the accessible lysine residues to react withselectivity.

In other embodiments, the PEG comprises a reactive ester such as anN-hydroxy succinimidate at the end of the PEG chain. Such anN-hydroxysuccinimidate-containing PEG molecule reacts with select aminogroups at particular pH conditions such as neutral 6.5-7.5. For example,the N-terminal amino groups may be selectively modified under neutral pHconditions. However, if the reactivity of the reagent were extreme,accessible-NH₂ groups of lysine may also react.

The PEG can be conjugated directly to an amino acid residues of theantibody, or through a linker. In some embodiments, a linker is added toan antibody polypeptide, forming a linker-modified antibody polypeptide.Such linkers provide various functionalities, e.g., reactive groups suchsulfhydryl, amino, or carboxyl groups to couple a PEG reagent to thelinker-modified antibody polypeptide.

In some embodiments, the PEG conjugated to the antibody polypeptide islinear. In other embodiments, the PEG conjugated to the antibodypolypeptide is branched. Branched PEG derivatives such as thosedescribed in U.S. Pat. No. 5,643,575, “star-PEG's” and multi-armed PEG'ssuch as those described in Shearwater Polymers, Inc. catalog“Polyethylene Glycol Derivatives 1997-1998.” Star PEGs are described inthe art including, e.g., in U.S. Pat. No. 6,046,305.

PEG having a molecular weight in a range of from about 2 kDa to about100 kDa, is generally used, where the term “about,” in the context ofPEG, indicates that in preparations of polyethylene glycol, somemolecules will weigh more, some less, than the stated molecular weight.For example, PEG suitable for conjugation to antibody has a molecularweight of from about 2 kDa to about 5 kDa, from about 5 kDa to about 10kDa, from about 10 kDa to about 15 kDa, from about 15 kDa to about 20kDa, from about 20 kDa to about 25 kDa, from about 25 kDa to about 30kDa, from about 30 kDa to about 40 kDa, from about 40 kDa to about 50kDa, from about 50 kDa to about 60 kDa, from about 60 kDa to about 70kDa, from about 70 kDa to about 80 kDa, from about 80 kDa to about 90kDa, or from about 90 kDa to about 100 kDa.

Preparing PEG-Antibody Conjugates

As discussed above, the PEG moiety can be attached, directly or via alinker, to an amino acid residue at or near the N-terminus, internally,or at or near the C-terminus of the antibody polypeptide. Conjugationcan be carried out in solution or in the solid phase.

N-Terminal Linkage

Methods for attaching a PEG moiety to an amino acid residue at or nearthe N-terminus of an antibody polypeptide are known in the art. In someembodiments, known methods for selectively obtaining an N-terminallychemically modified antibody are used. For example, a method of proteinmodification by reductive alkylation which exploits differentialreactivity of different types of primary amino groups (lysine versus theN-terminus) available for derivatization in a particular protein can beused. Under the appropriate reaction conditions, substantially selectivederivatization of the protein at the N-terminus with a carbonyl groupcontaining polymer is achieved. The reaction is performed at pH whichallows one to take advantage of the plc differences between the ϵ-aminogroups of the lysine residues and that of the a-amino group of theN-terminal residue of the protein. By such selective derivatizationattachment of a PEG moiety to the antibody is controlled: theconjugation with the polymer takes place predominantly at the N-terminusof the antibody and no significant modification of other reactivegroups, such as the lysine side chain amino groups, occurs.

C-Terminal Linkage

MonoPEGylation can be accomplished by using a PEG reagent that isselective for the C-terminus of a polypeptide, which can be preparedwith or without spacers. For example, polyethylene glycol modified asmethyl ether at one end and having an amino function at the other endmay be used as the starting material.

Preparing or obtaining a water-soluble carbodiimide as the condensingagent can be carried out. Coupling antibody with a water-solublecarbodiimide as the condensing reagent is generally carried out inaqueous medium with a suitable buffer system at an optimal pH to effectthe amide linkage. A high molecular weight PEG can be added to theprotein covalently to increase the molecular weight.

The reagents selected will depend on process optimization studies. Anon-limiting example of a suitable reagent is EDC or1-ethyl-3-(3-dimethylaminopropyl) carbodiimide. The water solubility ofEDC allows for direct addition to a reaction without the need for priororganic solvent dissolution.

Even though the use of PEG amine has been mentioned above by name orstructure, such derivatives are meant to be exemplary only, and othergroups such as hydrazine derivatives as in PEG-NH-NH₂ which will alsocondense with the carboxyl group of the antibody protein, can also beused. In addition to aqueous phase, the reactions can also be conductedon solid phase. Polyethylene glycol can be selected from list ofcompounds of molecular weight ranging from 300-40000. The choice of thevarious polyethylene glycols will also be dictated by the couplingefficiency and the biological performance of the purified derivative invitro and in vivo i.e., circulation times, anti viral activities etc.

Additionally, suitable spacers can be added to the C-terminal end of theantibody heavy chain and/or light chain protein. The spacers may havereactive groups such as SH, NH₂ or COOH to couple with appropriate PEGreagent to provide the high molecular weight Antibody derivatives. Acombined solid/solution phase methodology can be devised for thepreparation of C-terminal pegylated antibody polypeptides.

If desired, PEGylated antibody is separated from unPEGylated antibodyusing any known method, including, but not limited to, ion exchangechromatography, size exclusion chromatography, and combinations thereof.

Antibody-Fusion Proteins

The invention also contemplates recombinant antibodies having theantigen specificity of a SEAM3 MAb, where the antibody is modified toinclude a heterologous protein. For example, a SEAM3 heavy chainpolypeptide or SEAM3 light chain polypeptide may be joined to a reporterprotein or to a protein having a desired anti-cancer effect. Forexample, SEAM3 may be conjugated to a second antibody (or at least anantigen-binding portion thereof), e.g., an antibody that specificallybinds an angiogenic or proliferative factor, such as an antibody that isdirected against vascular enthothelial growth factor (VEGF), which iskey mediator of angiogenesis, where SEAM3 targets the conjugate tospecific cancer cells and the anti-VEGF antibody inactivates VEGF thusinhibiting angiogenesis.

In one embodiment, the invention provides a CDR of a SEAM3 light chainpolypeptide or a CDR of a heavy chain SEAM3 polypeptide which is linkedto a heterologous polypeptide, i.e., is linked to a polypeptide to whichit is not normally associated in the native SEAM3 antibody. Methods forproducing a fusion protein of interest when provided a nucleic acidsequence are well known in the art.

Methods for Producing Recombinant Antibodies

In many embodiments, the nucleic acids encoding a SEAM3 monoclonalantibody, or at least a CDR of a SEAM3 heavy chain polypeptide or atleast a CDR of a SEAM3 light chain polypeptide, are introduced directlyinto a host cell, and the cell incubated under conditions sufficient toinduce expression of the encoded antibody. Accordingly, the inventionalso contemplates recombinant host cells containing an exogenouspolynucleotide encoding at least a CDR of a SEAM3 heavy chainpolypeptide or at least a CDR of a SEAM3 light chain polypeptide.

Any suitable host cell, vector and promoter can be used in connectionwith the SEAM3-encoding nucleic acids of the invention. Of particularinterest are vectors having an insert encoding at least a CDR of a SEAM3heavy chain polypeptide and/or at least a CDR of a SEAM3 light chainpolypeptide. Also of interest are polynucleotides that are composed of anucleic acid sequence encoding at least a CDR of a SEAM3 heavy chainpolypeptide or at least a CDR of a SEAM3 light chain polypeptide, wherethe SEAM3-encoding sequence is operably linked to a heterologouspromoter. Exemplary host cells, vectors, and promoters will now bedescribed in more detail.

Any cell suitable for expression of expression cassettes may be used asa host cell. For example, yeast, insect, plant, etc., cells. In manyembodiments, a mammalian host cell line that does not naturally produceantibodies, e.g., mammalian cells that are not hybridoma cells, B cells,or spleen cells. It may also be of interest to use cells that providefor altered glycosylation of the recombinant antibody, or which lackglycosylation. Exemplary cells include, but are not limited to: monkeykidney cells (COS cells), monkey kidney CVI cells transformed by SV40(COS-7, ATCC CRL 165 1); human embryonic kidney cells (HEK-293, Grahamet al. J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCCCCL 10); chinese hamster ovary-cells (CHO, Urlaub and Chasin, Proc.Natl. Acad. Sci. (USA) 77:4216, (1980); mouse sertoli cells (TM4,Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CVI ATCCCCL 70); african green monkey kidney cells (VERO-76, ATCC CRL-1587);human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells(MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442);human lung cells (W138, ATCC CCL 75); human liver cells (hep G2, HB8065); mouse mammary tumor (MMT 060562, ATCC CCL 51); TRI cells (Matheret al., Annals N.Y. Acad. Sci 383:44-68 (1982)); NIH/3T3 cells (ATCCCRL-1658); and mouse L cells (ATCC CCL-1). Additional cell lines willbecome apparent to those of ordinary skill in the art. A wide variety ofcell lines are available from the American Type Culture Collection,10801 University Boulevard, Manassas, Va. 20110-2209.

In mammalian host cells, a number of viral-based expression systems maybe utilized to express a subject antibody. In cases where an adenovirusis used as an expression vector, the antibody coding sequence ofinterest may be ligated to an adenovirus transcription/translationcontrol complex, e.g., the late promoter and tripartite leader sequence.This chimeric gene may then be inserted in the adenovirus genome by invitro or in vivo recombination. Insertion in a non-essential region ofthe viral genome (e.g., region E1 or E3) will result in a recombinantvirus that is viable and capable of expressing the antibody molecule ininfected hosts (e.g., see Logan & Shenk, Proc. Natl. Acad. Sci. USA81:355-359 (1984)). The efficiency of expression may be enhanced by theinclusion of appropriate transcription enhancer elements, transcriptionterminators, etc. (see, e.g., Bittner et al., Methods in Enzymol.153:51-544 (1987)).

For long-term, high-yield production of recombinant antibodies, stableexpression may be used. For example, cell lines, which stably expressthe antibody molecule may be engineered. Rather than using expressionvectors which contain viral origins of replication, host cells can betransformed with immunoglobulin expression cassettes and a selectablemarker. Following the introduction of the foreign DNA, engineered cellsmay be allowed to grow for 1-2 days in an enriched media, and then areswitched to a selective media. The selectable marker in the recombinantplasmid confers resistance to the selection and allows cells to stablyintegrate the plasmid into a chromosome and grow to form foci which inturn can be cloned and expanded into cell lines. Such engineered celllines may be particularly useful in screening and evaluation ofcompounds that interact directly or indirectly with the antibodymolecule.

Methods of introducing nucleic acids into cells are well known in theart. Suitable methods include electroporation, particle gun technology,calcium phosphate precipitation, direct microinjection, and the like.The choice of method is generally dependent on the type of cell beingtransformed and the circumstances under which the transformation istaking place (i.e. in vitro, ex vivo, or in vivo). A general discussionof these methods can be found in Ausubel, et al, Short Protocols inMolecular Biology, 3rd ed., Wiley & Sons, 1995. In some embodimentslipofectamine and calcium mediated gene transfer technologies are used.

After the subject nucleic acids have been introduced into a cell, thecell is typically incubated, normally at 37° C., sometimes underselection, for a period of about 1-24 hours in order to allow for theexpression of the antibody. In embodiments of particular interest, theantibody is typically secreted into the supernatant of the media inwhich the cell is cultured.

Once a recombinant antibody molecule of the invention has been produced,it may be purified by any method known in the art for purification of animmunoglobulin molecule, for example, by chromatography (e.g., ionexchange, affinity, particularly by affinity for the specific antigenafter Protein A, and sizing column chromatography), centrifugation,differential solubility, or by any other standard technique for thepurification of proteins. In many embodiments, antibodies are secretedfrom the cell into culture medium and harvested from the culture medium.

Kits

Also provided by the invention are kits for practicing the methodsdisclosed herein, as described above. The kits can include one or moreof, depending upon the intended use of the kit, the compositionsdescribed herein, such as: a deNAc SA antigen, cells suitable for use inthe biosynthetic methods of de-N-acetylated PS production (optionally,with the acyl mannosamine and trihaloacyl mannosamine reagents describedin the methods above), an anti-deNAc SA epitope antibody, a nucleic acidencoding the same (especially a nucleic acid encoding a CDR of a heavyand/or light chain of SEAMS MAb), or a recombinant cell containing thesame. Other optional components of the kit include: buffers, etc., foradministering the anti-deNAc SA epitope antibody or deNAc SA antigen,and/or for performing a diagnostic assay. The recombinant nucleic acidsof the kit may also have restrictions sites, multiple cloning sites,primer sites, etc to facilitate their ligation to constant regions ofnon-SEAM3 encoding nucleic acids. The various components of the kit maybe present in separate containers or certain compatible components maybe precombined into a single container, as desired.

In addition to above-mentioned components, the subject kits typicallyfurther include instructions for using the components of the kit topractice the disclosed methods. The instructions for practicing thesubject methods are generally recorded on a suitable recording medium.For example, the instructions may be printed on a substrate, such aspaper or plastic, etc. As such, the instructions may be present in thekits as a package insert, in the labeling of the container of the kit orcomponents thereof (i.e., associated with the packaging or subpackaging)etc. In other embodiments, the instructions are present as an electronicstorage data file present on a suitable computer readable storagemedium, e.g. CD-ROM, diskette, etc. In yet other embodiments, the actualinstructions are not present in the kit, but means for obtaining theinstructions from a remote source, e.g. via the internet, are provided.An example of this embodiment is a kit that includes a web address wherethe instructions can be viewed and/or from which the instructions can bedownloaded. As with the instructions, this means for obtaining theinstructions is recorded on a suitable substrate.

Also provided by the subject invention are kits including at least acomputer readable medium including programming as discussed above andinstructions. The instructions may include installation or setupdirections. The instructions may include directions for use of theinvention with options or combinations of options as described above. Incertain embodiments, the instructions include both types of information.

The instructions are generally recorded on a suitable recording medium.For example, the instructions may be printed on a substrate, such aspaper or plastic, etc. As such, the instructions may be present in thekits as a package insert, in the labeling of the container of the kit orcomponents thereof (i.e., associated with the packaging orsubpackaging), etc. In other embodiments, the instructions are presentas an electronic storage data file present on a suitable computerreadable storage medium, e.g., CD-ROM, diskette, etc, including the samemedium on which the program is presented.

EXAMPLES

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

Example 1 Preparation of N-Acyl NMB PS and Derivatives Having a deNAc SAEpitope

N-acyl Neisseria meningitidis Group B (NmB) polysaccharide (PS)(acyl=acetyl [Ac] or propionyl [Pr]) was prepared by the method of Guoand Jennings, with differences as noted below (Guo, Z. and Jennings, H.in 2001. N-Propionylation. In Meningococcal Vaccines: Methods andProtocols. A. J. Pollard, and C. J. M. Maiden, eds. Humana Press Inc.,Totowa, N.J., p. 55.) as follows to produce PS derivatives having adeNAc SA epitope. Colominic acid or NmB PS (100 mg; EY Laboratories,Inc., San Mateo, Calif.) and 10 mg of sodium borohydride (Sigma-Aldrich)was dissolved in 10 ml of 2M NaOH and heated to 90° C. in a sealed tube(Pierce Chemical Co., Rockford, Ill.) for 2 h.

The conditions of the de-N-acetylation reaction differ from thosedescribed by Guo and Jennings Instead of producing a completelyde-N-acetylated PS derivative as described by Guo and Jennings, theproduct typically contained 20% N-acetyl residues as determined byresorcinol assay described below. Also, heating the solution to 100° C.and above and hydolysis times longer than 2 h results in degradation ofthe polysaccharide and production of undefined, undesirable sideproducts. FIG. 1 provides the structure of an exemplary de-N-acetylatedPS.

The approach described herein has advantages for preparing PSderivatives containing a mixture of N-acetyl and N-acyl residues (e.g.N-propionyl, N-butanoyl, etc.), as well as for preparing PS derivativescontaining a mixture of N-acetylated and de-N-acetylated residues, sinceit provides that a minimum of about 20% of the residues werede-N-acetylated. Also, the addition of sodium borohydride reduces theketone at the reducing end of the PS to an alcohol and also, an iminethat could be formed between the de-N-acetylated amino group and the C2ketone of the reducing end residue to a secondary amine NmB PSderivatives containing residues with N-acetyl groups, de-N-acetyl sites,and a cyclic secondary amine at the reducing end residue were bound bythe non-autoreactive, anti-N—Pr NmB PS mAb SEAM 3 (see Example 3, below)and, therefore, are important antigens for eliciting antibodies that arereactive with de-N-acetyl sialic acid antigens (in particular inpolymers of alpha (28) N-acetyl neruaminic acid) that are expressed incancer cells.

After cooling the solution to ambient temperature, the solution wasadjusted to pH 8.0 with 2 M HCl or glacial acetic acid, dialyzed againstwater, and lyophilized was re-acylated as described below withoutfurther purification.

Free amino groups were acylated by resuspending the PS (˜100 mg) in 3-5ml of water and adjusting the pH to 8-9 by adding 0.1 M NaOH and adding0.5 ml of acyl anhydride (e.g., acetic acid anhydride or propionic acidanhydride) in 5 aliquots with stirring over several hours. (Aceticanhydride was not included in the derivatives previously prepared by Guoand Jennings) Alternatively, the carboxylic acid was activated bycombining 0.5 ml of the acid with 1 equivalent of1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC, PierceChemical Company, Rockford, IL). A small amount of water (approximately1 ml) was added to completely dissolve the EDC. As with the anhydrides,the carbodiimide-activated carboxylic acid was added in 5 equal aliquotsover several hours with stirring. In some applications, such as inpreparing derivatives for use in conjugating to a carrier protein, forexample N-acryl, -methacryl, -bromoacetyl (BrAc)or -chloroacetyl (ClAc),as described below, the amount of carboxylic acid was reduced to afraction of the amount of fee amine in the polysaccharide (e.g. 10% to90%) as determined by resorcinol assay (as described below). Theadvantage of using the EDC-activated acylating reagents is that they donot hydrolyze as rapidly in water as the anhydrides or acyl chloridesand react more selectively with amines This permits better control overthe fraction of amino groups acylated. Since hydrolysis is slower, largefluctuations in pH, which can result in extensive hydrolysis of N-acryl,BrAc, and ClAc groups, are avoided. The pH of the solution wasmaintained at ˜8-9 by adding 2 M NaOH as required. The solution wasdialyzed and lyophilized.

Although most of the amino groups were acylated in this procedure(80%-90%), some amino groups were not derivatized and remain free aminogroups. PS containing residues with de-N-acetyl sites, including at thenon-reducing end of the polymer was bound by SEAM 3 (see Example 3,below) and is, therefore, an important determinant for elicitingprotective, non-autoreactive anti-NmB capsular antibodies.

Smaller fragments of the PS (average degree of polymerization [Dp]<20)were produced by hydrolysis in water at acidic pH. A portion of theN-acyl NmB PS (20 mg) was dissolved in 5 ml of 20 mM NaOAc, pH 5.5 andheated to 50° C. in a sealed tube for 1-24 h, typically 5 h, dependingon the size of the fragments desired.. The solution was dialyzed andlyophilized.

In addition to producing PS having a Dp that is on average smaller thanthat of the starting PS, acid treatment results in the formation oflactones between the Cl carboxyl group and the C9 OH group of thepreceding residue (FIG. 2). PS containing small amounts of lactone mayoccur in sialic acid antigens expressed in cancer cells. The presence ofsmall amounts of lactone in NmB PS derivative preparations mayfacilitate eliciting antibodies that are reactive with deNAc SA antigensexpressed on the surface of cancer cells.

Aldehyde groups were introduced into the non-reducing and reducing endsof the PS for use in covalent attachment to a carrier protein. The PS(20 mg) was dissolved in 1 ml of 0.1 M NaOAc buffer, pH 6.5. Sodium metaperiodate (5 mg, Sigma-Aldrich) was added and the solution kept in thedark for 30 min. The remaining NaIO4 was degraded by adding 0.1 ml of10% (wt/vol) ethylene glycol in water and left for 30 min This procedureproduces aldehyde groups at C8 and/or C7 . of the non-reducing endterminal residue and, for PS that contains a reducing end terminalresidue in which the C2 ketone was reduced to an alcohol duringde-N-acetylation (see above), an aldehyde group on C7 (FIG. 3).

Some fraction of de-N-acetyl residues were also oxidized to aldehydesusing periodate since the CS amino group is vicinal to the C4 hydroxylgroup. To minimize destruction of de-N-acetyl SA residues, which areepitopes recognized by SEAM 3, by periodate, N-Acryl, -BrAc, or -ClAcgroups were alternatively introduced into N—Pr and N-Ac NmB PS thatcontained de-N-acetyl residues as the result of de-N-acetylation andincomplete re-acylation. The carboxylic acid groups were activated withEDC as described above. Only a fraction of the free amines present inthe PS were acylated (10%-90%) by limiting the amount of activatedcarboxylic acid added to the reaction. The acryl, BrAc, and ClAc groupsare reactive with thiols and amino groups present in carrier proteinsunder mild conditions and thus, the PS derivatives can be conjugated toa carrier protein without the oxidative damage caused by treatment ofthe PS with periodate.

Preparation of Dodecylamine and Protein-PS Derivative Conjugates.

Dodecylamine derivatives were prepared by combining 20 milligrams of NmBPS derivative containing non-reducing end or reducing end aldehydes orketones with 10 milligrams of dodecylamine in 5 milliliters of water.After heating the mixture to about 50 degrees C. for 30 minutes withstirring, 5 mg of sodium cyanoborohydride was added. The mixture wasstirred at ambient temperature for 24 hours then dialyzed in water for 3to 5 days to remove excess dodecylamine

The reactivity of the dodecylamine derivatives with SEAM mAbs wasdetermined by direct binding ELISA in which the antigen (i.e. thedodecylamine PS derivative) was absorbed to the surface of a microtiterplate by incubating a solution of the antigen in PBS buffer in the wellof a microtiter plate overnight at 4 degrees C. The plates were washedwith PBS buffer (5×) and blocked with PBS buffer containing 1%(weight/weight) of bovine serum albumin (Sigma; blocking buffer) for 1hour at ambient temperature. The antibodies were diluted in blockingbuffer and added to the plate (100 microliters per well). Afterincubating the plate for 4 hours at ambient temperature, the plates werewashed with PBS buffer (5×) and rabbit anti-mouse-alkaline phosphataseconjugate antibody (Zymed) diluted in blocking buffer was added. Afterincubating an additional hour, the plates were washed (5×) with PBSbuffer and the bound antibody was detected by adding p-nitrophenylphosphate substrate in 50 mM sodium carbonate buffer, pH 9, containing 1mM MgCl₂. The absorbance at 405 nm after 30 minutes incubation atambient temperature was measured using a BioRad Model 550 microtiterplate reader. The results of binding experiments are shown in FIG. 34.

PS derivatives conjugated to a carrier protein were prepared bycombining 5 milligrams of bovine serum albumin (BSA, Pierce ChemicalCo.) tetanus toxoid with 10 mg of PS derivative or PS derivativecontaining terminal end aldehyde groups or N-Acryl, BrAc, or ClAc groupsin PBS buffer. 5 milligrams of sodium cyanoborohydride (PS containingaldehydes) or nothing (N-Acryl, -BrAc, -ClAc) was added and the mixturewas stirred in the dark for 5 days at ambient temperature. The solutionwas dialyzed (10-14 kDa cutoff membrane) in PBS buffer. The reactivityof the PS derivative-BSA conjugates with mAbs was determined by directbinding ELISA as described in the previous paragraph. The results ofbinding experiments are shown in FIG. 35.

The concentration of sialic acid and de-N-acetyl sialic acid in NmB PSderivative stock solutions was determined by the Svennerholm resorcinolreaction (Svennerholm, L. (1957) Biochim Biophys. Acta 24:604) modifiedas follows. Resorcinol working reagent was prepared by combining 9.75milliliters of water, 0.25 milliliters of 0.1 M CuSO4.5H2O, 10milliliters of 20 milligram per milliliter solution of resorcinol inwater, and 80 milliliters of concentrated HCl. The resorcinol workingreagent (300 microliters) was combined with the sialic acid orde-N-acetyl sialic acid sample solution (up to 50 micrograms of sialicacid) or standard stock solution in water (300 microliters) in apolypropylene deep well (2 milliliter) microtiter plate. The plate wassealed with a plate cover and heated in a boiling water bath for 30minutes. After cooling to ambient temperature, isoamyl alcohol (600microliters) was added and mixed using a pipette. The phases wereallowed to separate and the upper isoamyl alcohol layer was removed to aclean microtiter plate. 250 microliters of the isoamyl alcohol extractand the lower aqueous solution were transferred separately to apolystyrene microtiter plate and the absorbance at 495 nm and 580 nm wasmeasured.

The amount of N-acetyl sialic acid was determined by from the absorbanceof the isoamyl alcohol fraction at 580 nm and the amount of de-N-acetylsialic acid was determined from the absorbance of the aqueous fractionat 495 nm in comparison to a standard curve for each. The amount ofde-N-acetyl sialic acid was corrected for the amount of de-N-acetylationthat occurs during the acid hydrolysis step of the assay by measuringthe amount of de-N-acetylation that occurs in the sialic acid standard.

Reverse-Phase HPLC purification of NmB PS derivatives containing longchain alkyl groups. NmB PS derivatives containing long chain (i.e. ≥C8)alkyl groups (e.g. dodecylamine derivatives) were separated byreverse-phase HPLC using a Poros RUH column and BioCAD PerfusionChromatography Workstation. Derivatives were eluted with a gradient from0% to 80% acetonitrile in 20 mM ammonium acetate buffer, pH 6.5 over 30minutes at a flow rate of 5 milliliters per minute. Fractions (1milliliter each) were collected.

Fractions containing derivatives that were reactive with mAbs (forexample SEAM 3, SEAM 12 Granoff et al. 1998, supra) were determined byadding 100 microliters of each fraction to a well of a 96 wellmicrotiter plate (Immulon II, Dynatech) and incubating the plate at 4degrees C. overnight. The plates were washed with PBS buffer (5×) andblocked with PBS buffer containing 1% (weight/weight) of bovine serumalbumin (Sigma; blocking buffer) for 1 hour at ambient temperature. Theantibodies were diluted in blocking buffer and added to the plate (100microliters per well). After incubating the plate for 4 hours at ambienttemperature, the plates were washed with PBS buffer (5×) and rabbitanti-mouse-alkaline phosphatase conjugate antibody (Zymed) diluted inblocking buffer was added. After incubating an additional hour, theplates were washed (5×) with PBS buffer and the bound antibody wasdetected by adding p-nitrophenyl phosphate substrate in 50 mM sodiumcarbonate buffer, pH 9, containing 1 mM MgCl₂. The absorbance at 405 nmafter 30 minutes incubation at ambient temperature was measured using aBioRad Model 550 microtiter plate reader.

MALDI-TOF mass spectroscopy of non-reducing end dodecylamine derivativesof NmB PS. The solvent in fractions obtained from reverse-phase HPLCwere evaporated using a SpinVac (ThermoSavant). The residue wasdissolved in acetonitrile/water (1:1). A matrix oftrihydroxyacetophenone (THAP) at a concentration of 3 milligrams permilliliter in acetonitrile/water was spotted onto the target (0.5microliter per spot). After drying the matrix spots under vacuum, thesample was spotted on top of the matrix spot (0.5 microliters).MALDI-TOF (Autoflex, Bruker Daltonics) was performed in the bothpositive and negative linear modes (30 shots N₂ laser, 50% laser power)and in reflector positive and negative modes (30 shots N₂ laser, 50%laser power). The mass spectra were calibrated using external peptide(Bruker Daltonics) and sialic acid (EY Laboratories) standards. Theerror of the observed masses were estimated to be ≤0.1%. FIGS. 16-18show structures identified by MALDI-TOF from a preparation of NmB PSthat were reactive with protective, non-autoreactive anti-NmB capsularmAb SEAM 3 and purified by reverse-phase HPLC as described above. Thederivatives contain a mixture of de-N-acetyl, N-acetyl, and N-propionylresidues with at least one de-N-acetyl residue.

Example 2 Determination of the Structure of NMB PS DerivativesRecognized by Seam 3 by Maldi-TOF Mass Spectroscopy

SEAM 3 was linked to magnetic beads as follows. MagnaBind™ goatanti-mouse IgG beads (200 μl; Pierce) were combined with 5 μg of SEAM 3in PBS buffer. The mixture was incubated at ambient temperature on arotating wheel for 1 hr. The beads were washed 3 times with wash buffer.The bound antibody was cross-linked to the beads by adding BS³™ (Pierce)to a concentration of 2 mM in PBS buffer and mixed by vortexing for 30min at ambient temperature. Unreacted BS³™ was degraded by adding Tristo 0.1 M, pH 8.0 for 10 min. The beads were washed 3 times with PBSbuffer. N—Pr NmB PS (240 micrograms) prepared in Example 1 was added tothe washed beads in PBS buffer. After incubating the mixture on arotating wheel for 1 h at ambient temperature, the unbound material wasremoved and the beads washed 2 times with wash buffer and once with PBSbuffer then resuspended in 200 μl of PBS buffer. Neuraminidase (0.00175U, EC3.2.1.18; Sigma) was added to each tube and the mixture incubatedovernight at 37 degrees C. on a rotating wheel. The bound PS isheterogeneous with respect to Dp, therefore, the bead-antibody-PScomplex was treated with neuraminidase, which sequentially removesresidues from the non-reducing end of the polymer, to reduce the size ofthe polymer to the length that can be protected from further digestionby the antibody. After the neuraminidase treatment, the beads werewashed 3 times with 50 mM ammonium carbonate buffer, pH 8.5 and thebound PS was finally eluted with 0.1 M triethylamine in water.

For analysis by matrix assisted laser desorption ionization time offlight (MALDI-TOF) mass spectroscopy, the solution of eluted PS andtriethylamine/water was removed by evaporation in a Spin-Vac (Savant).Dried sample was resuspended in 4 μl of 50% (vol/vol)acetonitrile/water. The matrix, a saturated solution of2′,4′,6′-trihydroxyacetophenone (THAP, Fluka Chemical) in 50%acetonitrile/water (0.5 μl), was spotted on a stainless steel targetplate. PS sample (2 times, 0.5 μl) was spotted on top of the dried THAPspot. The samples were analyzed using a Bruker Autoflex MALDI-TOF massspectrometer operating in the negative ion reflector mode.

FIG. 4 shows a representative mass spectrum of PS derivatives bound bySEAM 3 after neuraminidase treatment. FIG. 5 shows the observed massesfor each sample and the theoretical masses of corresponding ions thatare consistent with the observed masses. The structures of PSderivatives are shown in FIGS. 6 to 15. All of the masses correspond toa disaccharide containing one or more residues in which the N-acetylgroup on the C-5 amino group has been removed.

Example 3 Analysis of deNAc SA Epitope-Containing N-PR NMB PSDerivatives that Bind to Seam 3 by Sialidase A Digestion and HighPerformance Anion Exchange Chromatography with Pulsed AmpermetricDetection (HPAC-PAD),

The exo sialidase from Arthrobacter ureafaciens (SIALIDASE A™, Prozyme,Hayward, Calif.) cannot degrade polysialic acids (N—Ac or N—Prderivatives) that terminate on the non-reducing end with a de-N—Acsialic acid residue. Therefore, exhaustive digestion of a preparation ofNmB PS or N—Pr NmB PS that contains de-N-acetyl residues randomlylocated throughout the polymer with sialidase A will result inconversion of the polysialic acid to 5-N-acyl neuraminic acid exceptwhen the sialidase encounters a de-N-acetyl residue. At that point, nofurther degradation of the polymer will occur. Also, the sialic acidmolecules that are not degraded have a de-N-acetyl sialic acid residueat the non-reducing end. To confirm the results presented in Example 2that SEAM 3 binds to a mixture of de-N-acetyl and N-acyl residues,preparations of colominic acid (EY Laboratories) and N—Pr NmB PS (10 mgeach) were suspended in 50 mM NaOAc buffer, pH 6.5. SIALIDASE A™ (0.1 U,Prozyme) was added and the solutions were incubated at 37° C. for 3days.

The fraction of N—Ac NmB oligosaccharide (OS) and polysaccharide (PS)and N—Pr NmB OS and PS remaining after sialidase treatment and thedegree of polymerization were quantified by HPAC-PAD. The sample wasinjected into a Dionex (Sunnyvale, Calif.) liquid chromatograph fittedwith a GP40 Gradient Pump, PA200 column equilibrated with 0.1 M NaOH(93%) and 0.1 M NaOH containing 1M NaOAc (7%) and an ED40Electrochemical Detector. Saccharides were eluted with a linear gradientbeginning from the initial conditions to 100% 0.1 M NaOH/1M NaOAc.Saccharides eluting from the column were detected by pulsed ampermetricdetection using the ED40 Electrochemical Detector.

The resulting chromatogram showed that from about 81% to 88% of both PSshad been degraded to N—Ac or N—Pr neuraminic acid, respectively, withthe remaining about 12-19% composed mainly of oligosaccharide having aDp of from about 2 to about 18 (FIG. 36) and very small amounts ofhigher molecular weight polymers. The HPAC-PAD analysis shows that bothcolominic acid and N—Pr NmB PS preparations contain de-N-acetyl residueseven though the colominic acid preparation had not be subjected tode-N-acetylation/re-acylation procedures.

The ability of colominic acid and N—Pr NmB PS to inhibit binding of SEAM3 to in an ELISA was compared to sialidase A-treated colominic acid andN—Pr NmB PS prepared as described above. The wells of microtiter plates(Immulon 2; Dynatech Laboratories, Inc.) were coated with N—Pr NmBPS-dodecylamine (prepared as described in Example 1) in phosphatebuffered saline (PBS; pH 7.4). The plates were incubated overnight at 4°C. After washing three times with PBS, the wells were filled with 200 μlof blocking buffer (PBS containing 1% bovine serum albumin [BSA, Sigma]and 0.1% sodium azide; [pH 7.4]) and then incubated for 30-60 min atroom temperature to block nonspecific binding sites. The plates werewashed three times with PBS buffer. Inhibitors were serially diluted inblocking buffer on the plate in total final volume of 50 SEAM 3 dilutedin blocking buffer to a concentration that produced an OD405 nm of 0.5when developed with substrate was added to the wells in a volume of 50The plates were covered and incubated overnight at 4° C. On thefollowing day the wells were washed four times with PBS buffer and wereincubated for 2 h at ambient temperature with 100 μl/well of alkalinephosphatase-conjugated anti-mouse polyclonal antibody (IgA+IgG+IgM;Zymed) diluted 1:3000 in blocking buffer. The plates were then washedwith PBS buffer, and 100 μl of freshly prepared substrate (p-Nitrophenylphosphate; Sigma) diluted to 1 mg/ml in substrate buffer in 50 mM sodiumcarbonate buffer, pH 9, containing 1 mM MgCl₂. The absorbance at 405 nmafter 30 minutes incubation at ambient temperature was measured using aBioRad Model 550 microtiter plate reader. The relative activity of eachsample was compared by determining the dilution required to decrease theabsorbance at 405 nm by 50% of the absorbance observed in wellscontaining SEAM 3 but no inhibitor.

When measured by inhibition ELISA, the colominic acid preparation hadapproximately 200-fold less activity for binding to SEAM 3 than N—Pr NmBPS. However, there was no significant difference in the activity of theexosialidase-treated colominic acid or N—Pr NmB PS compared to theuntreated preparations even though more than 80% of the PS had beenconverted to monomeric N-acyl neuraminic acid as determined by HPAC-PAD.The results clearly shows that the epitope recognized by SEAM 3 iscomposed of a mixture of de-N-acetyl and N-acyl residues but not NmB PSderivatives that do not contain de-N-acetyl residues. Since the Dpcharacterized by HPAC-PAD varies between 2 and about 27, the de-N-acetylresidues can occur internally within the polymer or at the non-reducingend.

The amount of antigen recognized by SEAM 3 in preparations of colominicacid or N—Pr NmB PS is not affected by exhaustive digestion withexosialidase while non-reactive molecules in the preparations that donot contain de-N-acetyl residues are degraded. Therefore, exhaustiveexosialidase treatment of provides a means to greatly enrich colominicacid and N—Pr NmB PS preparations for molecules that bind to the mAb.

Example 4 Preparation of Vaccine Containing PS Derivatives Enriched withRespect to deNAc SA Antigens

The following provides an example of a method for producing a deNAc SAantigen-containing vaccine from PS using both the sialidase-basedenrichment method and generation of a conjugate by reaction with andlinkage through an acryl- or haloacetyl-group.

De-N-acetylation. Colominic acid (100 mg, EY Laboratories) and 10 mg ofsodium borohydride (Sigma-Aldrich) are dissolved in 10 ml of 2M NaOH,placed in a sealed glass hydrolysis tube (Pierce) and heated to 90° C.for 2 h. The solution is allowed to cool to ambient temperature andglacial acetic acid is added to lower the pH of the solution toapproximately 7. The solution is dialyzed (1 kDa cutoff) in 2×4L ofwater and lyophilized

Re-N-acylation. The de-N-acetylated NmB PS is resuspended in 5 ml ofwater and the pH adjusted to 8-9 with 2M NaOH. Acyl anhydride (e.g.acetic anhydride or propionic anhydride) is added in 5 portions of 0.1ml over a period of several hours with stirring. The pH is monitoredwith a pH meter and is adjusted to 8-9 with 2M NaOH as needed. Thesolution is dialyzed in water as before and lyophilized. The re-acylatedNmB PS typically contains 10%-30% de-N-acetyl sialic acid as determinedby resorcinol assay (vide supra). The product is enriched with respectto antigens that are reactive with SEAMS by treatment with SIALIDASE A™(Prozyme).

Sialidase treatment. The lyophilized powder is resuspended in 1 ml of 50mM sodium acetate buffer, pH 6.5. (1U) is added add the solution isincubated at 37° C. for 3-7 days. The progress of the reaction ismonitored by periodic HPAC-PAD analysis of a small portion of thereaction mixture that if first filtered through a Centricon membrane (30kDa cutoff, Millipore) to remove the . When no further release of5-N-acyl neuraminic acid occurs, the reaction is terminated and cycliclactones are hydrolyzed by increasing the pH of the reaction to 12 with2M NaOH for 1 h, neutralizing with glacial acetic acid, filteringthrough a 30 kDa Centricon membrane, dialyzing in water (1 kDa dialysistubing), and lyophilizing the product.

N-acylation with acrylic acid (or haloacetic acid). Thesialidase-treated partially de-N-acetylated NmB PS is resuspended inwater and the pH is adjusted to 8-9 with 2M NaOH. An amount of acrylicacid (or haloacetic acid) equal to from 10% to 100% of the amount ofde-N-acetyl sialic acid present in the preparation of re-N-acylated NmBPS (typically 40%-50% of the total amount of sialic acid determined byresorcinol assay) is combined with 0.9 equivalent of EDC (Pierce). Asmall amount of water is added as necessary to dissolve the EDC. Thesolution of activated acrylic acid (or activated haloacetic acid) isadded to the preparation of partially re-N-acylated NmB PS with stirringand the pH is maintained to 8-9 by adding 2M NaOH as necessary. Althoughan amount of activated acrylic acid (or activated haloacetic acid) equalto the amount of de-N-acetyl sialic acid can be added to the reaction,some amount of de-N-acetyl sialic acid will remain since some of theactivated acrylic acid will hydrolyze. After stirring for 1 h, thereaction mixture is dialyzed and lyophilized as described above. Theproduct is stored sealed under argon in the dark at −80° C. until usedfor conjugation to a carrier protein.

Conjugation to a carrier protein. The carrier protein (10 mg) isdissolved in 50 mM HEPES, pH 8.0, containing 150 mM NaCl. Theacyl-containing NmB PS preparation is added (20 mg) and the solutionleft standing at ambient temperature in the dark for 2 days. Thesolution is then dialyzed in PBS buffer using a dialysis membrane havinga mass cutoff of 30 kDa. The dialyzed conjugate is finally sterilefiltered (0.2μ) and stored at 4° C. until used. The amount of sialicacid conjugated to the protein is determined by resorcinol assay andconformation that the PS is covalently linked to the protein isdetermined by SDS-PAGE and Western blot detection with SEAMS.

Example 5 Biosynthetic Incorporation of N-Trichloroacetyl (orTrifluoroacetyl) Protected Sialic Acid Residues into Bacterial PS andUse of the Resulting Capsular PS to Prepare PS-Protein ConjugateVaccines

0 5 millimole (108 milligrams) of mannosamine hydrochloride wasdissolved in 10 milliliter of methanol containing 0.55 millimole ofsodium methoxide and cooled to 4 degrees C. 0 6 millimole oftrichloroacetic anhydride (or ethyl trifluoroacetate) was added and themixture stirred for 2 hrs. The progress of the reaction was monitored byspotting the reaction mixture on a silica gel TLC plate, developing theplate with ethylacetate, methanol, water (5:2:1) and detecting thedisappearance of mannosamine at the origin with iodine vapor or nihydrinreagent with heating. At the completion of the reaction, 1 5milliequivalents of AG 501-8× mixed bed resin (BioRad) and 10milliliters of water was added, the pH was adjusted to 7 by adding NaOHor HCl as needed and the mixture gently shaking for 1 hour. The solventmixture and beads were separated and the solvent was removed bylyophilization. Further purification of the product, if necessary, wasperformed by silica gel chromatography using the same solvent systemdescribed for TLC. Solvent from the combined fractions containing thedesired material was removed by evaporation. Finally, the dried productwas resuspended in water and lyophilized.

The trihaloacetylated mannosamine was incorporated into NmB PS byinoculating colonies of NmB strain M7 grown overnight at 37 degrees C.in 5% carbon dioxide on a freshly streaked chocolate agar plate to anOD620nm of 0.1 in Muller-Hinton broth supplemented with 5 millimolarN-acyl mannosamine For example, N-acetyl, -trichloroacetyl,-trifluoroacetyl mannosamine Stain M7 contains a transposon theinterrupts the gene encoding N-acetyl-D-glucosamine-6-phosphate 2epimerase (Swartley et al. 1994, J. Bact. 176:1530; Swartley et al.1996, J. Bact. 178:4052). As a result, the bacteria cannot synthesizecapsule PS unless the growth media was supplemented with N-acetylmannosamine Therefore, the N-acyl content of the capsule PS synthesizedin this system can be determined by the N-acyl or mixture of N-acylmannosamine provided in the growth media. The bacteria were grown at 37degrees C. to an OD620 nm of overnight).

Mutants of E. coli K1 can also be used in this production method in lieuof an NmB strain. Suitable E. coli K1 mutants that are deficient incapsular PS can be generated by, for example, knocking out expression ofa functional neuC gene product. Since, neuC encodes anN-acetyl-D-glucosamine-6-phosphate 2 epimerase , E. coli strainsdeficient in this gene can not synthesize capsular PS, and thus aresuitable for use in this method of PS derivative production.

The production of capsule PS containing the trihalo acetyl groups wasdemonstrated by fluorescence microscopy using the mAb SEAM 12 (Granoffet al. (1998) J Immunol 160, 5028-36) to detect the presence of capsulePS on the M7 producing strain. The results are shown in FIG. 37. Bindingof SEAM 12 to M7 supplemented with N-acetyl mannosamine is shown in FIG.37 (panel A) where binding is indicated by the presence of redfluorescence (shaded gray in the figure) of the detecting,rhodamine-labeled secondary antibody (Zymed). There is no binding ofSEAM 12 to M7 without N-acyl mannosamine or with N-trichloroacetylmannosamine supplement (FIG. 37, panels B and C). SEAM 12 does not bindto the capsule PS containing the trichloroacetyl groups because thelarge size of the trichloromethyl group disrupts binding. However, SEAM12 does bind to the capsule PS containing N-trifluoroacetyl groups (FIG.37, panel D, shaded gray in the figure) since the trifluoromethyl groupis nearly the same size as the methyl group of the N-acetyl derivative.

The polysaccharide was purified from the growth media as described byGuo and Jennings (Guo, Z. and Jennings, H. in 2001. In MeningococcalVaccines: Methods and Protocols. A. J. Pollard, and C. J. M. Maiden,eds. Humana Press Inc., Totowa, N.J., p. 41). The purifiedpolysaccharide was oxidized, conjugated to carrier proteins or fattyamines by reductive amination as described above, and the trihaloacetylgroups were removed by reduction with sodium borohydride. The finalproduct was purified by size exclusion chromatography as describedabove, dialyzed in PBS, and lyophilized.

Example 6 Biosynthetic Incorporation of N-trichloroacetyl (orTrifluoroacetyl) Protected Sialic Acid Residues Into Gangliosides andUse of the Resulting Gangliosides to Prepare Protein Conjugate Vaccinesand Outermembrane Vessicle Vaccines

1 g of mannosamine hydrochloride (4.5 mmol) was dissolved in 50 ml ofmethanol containing an equivalent of sodium methoxide and cooled to 4°C. 5.1 millimole of trichloroacetic chloride (or ethyl trifluoroacetate)was added and the mixture stirred for 2 hrs. Additional sodium methoxidewas added as needed to maintain the pH at ˜8. The progress of thereaction was monitored by spotting the reaction mixture on a silica gelTLC plate, developing the plate with ethylacetate, methanol, water(5:2:1) and detecting the disappearance of mannosamine at the originwith iodine vapor. At the completion of the reaction, the solvent wasremoved by evaporation. After triturating the remaining solid with 5 mlof methanol, the N-trihaloacetyl derivative was crystallized frommethanol/chloroform.

SK-Mel-28 cells were grown on square 245 mm×245 mm bioassay dish(Corning) until near confluent. Growth medium (RPMI supplemented with 5mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids,10% fetal bovine serum, and antibiotics) was replaced with growth mediumcontaining trichloroacetyl mannosamine (5 mM) for 24 hours, after whichcells were washed three times with PBS and lysed by hypotonic shock indistilled water (lhour at 4° C.). This was followed by 3 cycles offreeze/thawing using ethanol on dry ice/37° C. water bath. The crudemembrane fraction was pelleted by centrifugation at 4500 g for 20minutes at 4° C. The pellet was lyophilized and the lipids extracted bystepwise washing with methanol/chloroform (1:2, 1:1, 2:1 by volume) for30 minutes (Geilen et al 1992, Arch. Biochem. Biophys. 296, 108-114).The organic phase was dried under a steady stream of oxygen-freenitrogen gas and resuspended in 200 μl of chloroform/methanol/0.02%CaCl₂ (50:40:10).

De-N-acyl GM3 and GD3 (Calbiochem) were prepared by suspending 1 mg ofganglioside in 2 ml of 2.5 M tetrabutylammonium hydroxide and 3 ml ofbutanol then heating the mixture to >100 degrees C. for 4 hours. Aftercooling the mixture to ambient temperature, the pH was adjusted to about7 by adding 2 M HCl and the butanol removed by evaporation under astream of N₂. The remaining aqueous layer was dialyzed (1K cut-offdialysis tubing) against PBS buffer and used without furthermodification as an antigen for ELISA.

Lipids in the extract and in chemically de-N-acylated GD3 were analyzedby separation on high performance thin layer chromatography (HPTLC) andWestern blot. Samples of the ganglioside extract, the gangliosideextract that had been treated with sodium borohydride (1 mg/100 μl atambient temperature for 2 h) to remove the trichloroacetyl protectinggroup, and chemically de-N-acylated GD3 were spotted onto analuminum-backed silica gel 60 HPTLC plate (Merck) and the platedeveloped in chloroform/methanol/0.02% CaCl₂ (50:40:10). Plates used forWestern blot were dried and dipped in a solution of 0.4%polyisobutylmethacrylate in hexame/chloroform (21:8) for 1 min. Theplates were blocked with 1% bovine serum albumin (BSA) in PBS buffercontaining 0.1% sodium azide. MAbs (5 μg/ml) in the same blocking bufferwere incubated with the plates at 4° C. overnight. The plates werewashed 3 times in PBS buffer then incubated with goat anti-mouse Ig-HRPconjugate (Zymed) in PBS containing 1% BSA. After washing the plates 3times with PBS, substrate (HRP Chemiluminescence Reagent Plus fromPerkin-Elmer) was added to develop the plates. The luminescent image wascaptured on film.

Western blot to evaluate the reactivity of an anti-de-N-acyl GD3 mAbwith de-N-acetyl sialic acid gangliosides prepared chemically orbiosynthetically was performed with either GAG2 (Lanes 1-3, FIG. 38) orSEAM 3 (Lanes 4-6, FIG. 38). GAG2 is a murine monoclonal antibody (IgM)prepared to de-N-acyl GD3 by immunizing mice with N. meningitidis outermembrane vesicles (strain H44/76 in which the siaD gene has beeninactivated) containing de-N-acyl GD3 (EXAMPLE 9). The vesicles wereprepared as described below. GAG2 binds to de-N-acyl GD3 but not tore-N-acetylated GD3. Lanes 1 and 3 are gangliosides obtained fromtreatment of GD3 with tetrabutyl ammonium hydroxide (i.e. chemicalde-N-acylation). Lanes 2, 3, 5 and 6 are gangliosides extracted fromSK-MEL-28 cells grown in media supplemented with N-trichloroacetylmannosamine (i.e. biosynthetic N-protected sialic acid containinggangliosides). The lipid extract in lanes 2 and 5 was treated with NaBH₄to remove the trichloroacetyl protecting group to produce thede-N-acetyl sialic acid gangliosides. Lanes 3 and 6 contain the samelipid extract that has not been treated with NaBH₄. SEAM 3 does notreact with any of the de-N-acyl gangliosides produced by alkalitreatment. GAG2 reacts with a de-N-acetyl sialic acid gangliosideproduced biosynthetically that moves with the solvent front (lane 2)while SEAM 3 reacts with a different slower moving de-N-acetylganglioside derivative (lane 5). The lack of reactivity with both mAbswith lipid extract run in lanes 3 and 6 shows that the N-trichloroacetylprotecting group remains intact during the isolation procedure and thatde-N-acetyl sialic acid ganglioside derivatives are produced afterremoval of the protecting group with NaBH₄.

The results in FIG. 38 demonstrate that SEAM 3 binds to de-N-acetylsialic acid gangliosides prepared by biosynthesis ofN-trichloroacetyl-protected gangliosides in SK-MEL-28 cells followed byremoval of the protecting group with NaBH₄ (lane 5) but not to theprotected derivative (lane 6) or to chemically de-N-acylated GD3 (lane6). In addition, a mAb that is specific for de-N-acylated GD3 preparedby alkali treatment (GAG2) reacts with a different, faster movingderivative in the NaBH₄-treated SK-MEL-28 lipid extract. Thus, themethods described here can be used to selectively prepare gangliosidederivatives for use as vaccine and diagnostic antigens that are reactivewith mAbs, such as SEAM 3, that recognize de-N-acetyl sialic acidresidues and have cytotoxic functional activity against cancer cellsthat express de-N-acetyl sialic acid antigens.

Example 7 Preparation of deNAc Sa Antigens—Ganglioside DerivativesHaving a Mixture of N-Acetyl and De-n-acetyl Sialic Acid Residues

N-trichloroacetyl/N-acetyl sialic acid ganglioside derivatives obtainedby biosynthesis in SK-MEL-28 cells were solubilized inchloroform/methanol/0.02% CaCl₂. The N-trichloroacetyl amine protectinggroup was removed by reduction with sodium borohydride (1 mg NaBH₄/10 mgof crude lipid extract). Calcium borate that precipitated from thereaction was removed by centrifugation. The lipid derivatives wereseparated by HPTLC. The band containing material reactive with SEAM 3was scraped from the plate and extracted with chloroform/methanol (1:1).After removing the silica gel by centrifugation, the solvent from theextracted band was dried under N₂.

Outer membrane vesicles were prepared from Neisseria meningitidis groupB strain H44/76 in which the sialyl transferase gene siaD has beeninactivated. Cells from 1 litre of H44/76 grown in Muller-Hinton brothto an A620 nm of 0.6 were pelleted by centrifugation at 10,000xg for 30min. The cell pellet was resuspended in 0.1M Tris-HCl, pH8.6, containing10 mM EDTA and 0.5% DOC with the ratio of buffer to biomass of 5:1(v/w). The supernatant was collected after centrifugation (20,000×g; 30minutes; 4° C.) and the extraction was repeated with buffer volumereduced to one third. The combined supernatants were ultracentrifuged(125,000×g; 2 hrs; 4° C.), and the OMV pellet resuspended in 50 mMTris-HCl buffer, pH 8.6, containing 2 mM EDTA, 1.2% DOC and 20% sucrose.The protein concentration was determined using a standard protein assay(BCA, BioRad). The vesicle preparation and Empigen (1% w/v; Calbiochem)was added to the lipid film and sonicated with a bath sonicator(Branson) for 30 min then left to stir overnight at 4° C. The mixturewas then dialyzed exhaustively in PBS buffer for 5 days. The resultingOMV/ganglioside complexes were sterile filtered and frozen until usedfor vaccination.

Example 8 Preparation of N-trihaloacetyl/N-acetyl Sialic AcidGanglioside-Protein Conjugate Vaccine

The crude lipid fraction from the biosynthesis ofN-trihaloacetyl/N-acetyl sialic acid gangliosides in SK-MEL-28 cells waspurified by HPTLC, and the N-trihaloacetyl/N-acetyl sialic acidganglioside derivatives were extracted from the plate as described inExample 7. After removing the silica gel by centrifugation, an aldehydegroup was generated in the ganglioside by ozonolysis of the sphingosinedouble bond. The aldehyde was purified by reverse phase HPLC (WatersBondpak C18 microbore) and coupled to tetanus toxoid by reductiveamination with sodium cyanoborhydride. An excess of sodium borohydridewas added to the same reaction mixture to remove the N-trihaloacetylprotecting group. The reaction mixture was dialyzed in PBS buffer,sterile filtered, and frozen until used for immunization.

Example 9 Purification of SEAM 3 MAB

Solid sodium sulfate (Sigma-Aldrich Chemical Co., Saint Louis, Mo.) wasadded to a solution of SEAM 3 in PBS buffer (concentration of antibodyapproximately 30 micrograms/ml as determined by antibody capture assay(SouthernBiotech, Birmingham, Ala.)) to a final concentration of 0.5 M.After completely dissolving the solid sodium sulfate, the solution wasincubated approximately 18 hrs at 4° C. The solution was centrifuged(10,000xg) to remove precipitates and filtered (0.2μ). The antibody wasthen purified by size exclusion chromatography on a Toyopearl HW55Fcolumn (Supelco, Bellefonte, PA; 1.5 mm×25 mm) equilibrated with PBSbuffer containing 0.5 M sodium sulfate. Fractions containing activeantibody were determined by ELISA using N-propionyl NmB PS-dodecylamine(vide supra) as a solid phase antigen and detection using alkalinephosphate conjugated to rabbit anti-mouse IgA,G,M (H and L) (Zymed,South San Francisco, CA) and developed 4-nitrophenyl phosphate substrate(Sigma-Aldrich). Fractions containing active antibody were combined anddialyzed against PBS, sterile filtered (0.2μ) and stored at 4° C.Antibody concentrations of purified antibodies were determined byantibody capture assay (Southern Biotech).

Purified SEAM 3 was used in the Examples below.

Example 10 Presence of SEAM 3 Reactive Antigen in Cancer Cells andAbsence in Normal Cells

To determine whether there is a difference in expression of SEAM3-reactive antigen between normal melanocytes and melanoma tumor cells,immuno-staining of thin sections of each type of tissue were performed.In addition to SEAM 3, controls included the secondary antibody aloneand R24, which binds to the ganglioside GD3 that is expressed in normalmelanocytes and is overexpressed in some melanomas (Dippold et al. ProcNatl Acad Sci USA, 1980. 77(10): 6114-8.; Graus, et al., Brain Res,1984. 324(1): 190-4; Houghton et al. Proc Natl Acad Sci USA, 1985.82(4):1242-6; Panneerselvam et al. J Immunol, 1986. 136(7): 2534-41;Real et al. Cancer Res, 1985. 45(9): 4401-11; Vadhan-Raj et al. J ClinOncol, 1988. 6(10): 1636-48; Welt t al. Clin Immunol Immunopathol, 1987.45(2): 214-29).

The tissue sections were made from frozen samples of normal skin(HuSkinTb111 in FIG. 39) and two human melanomas (HuMe11151 andHuMe14034). To prevent the possibility of blocking de-N-acetyl antigenor extracting a lipid containing the antigen, the sections were preparedfrom frozen tissue and were dried onto the slides but not fixed withaldehydes or organic solvents (Chammas et al. Cancer Res, 1999. 59(6):1337-46). Endogenous peroxidases were removed by incubation in 0.03%peroxide for 30 min., followed by buffer washes and then endogenousbiotin was blocked using the Avidin/Biotin blocking kit from Vector Labs(Burlingame, CA). Non-specific binding to collagen was blocked with 1%BSA/PBS. BSA, or the mAbs R24 or SEAM 3 were then incubated in a humidchamber. Unbound antibody was removed by buffer rinses. Bound antibodywas then detected using the DAKO LSAB kit following the manufacturer'sdirections (Thermo Fisher Scientific, Waltham, Mass.). After additionalwashes, nuclei were counterstained using Mayer's hematoxylin (VectorLabs).

The results at 400× magnification are shown in FIG. 39 Immunostaining ofnormal human skin shows that anti-GD3 mAb R24 identifies melanocytes(arrows) as well as some neural twigs in the dermis of the skin. SEAM 3binds to an antigen in neural like structures of the dermis but is notpresent in melanocytes Staining of the two melanomas shows that R24reacts strongly with some but not all cells. In contrast, SEAM 3staining is weaker but nearly all of the melanoma cells are stained, asindicated by darkly shaded areas. The SEAM 3 staining appears to begranular and intracellular in the melanomas cells. Thus, the antigenrecognized by SEAM 3 is not detectably present in normal melanocytes butis present in human melanoma tumors. Based on fluorescence microscopyand cytotoxicity against SK-MEL-28 melanoma, CHP-134 neuroblastoma, andJurkat cells (acute lymphoblastic T-cell leukemia) described below (videinfra), the antigen is present on the cell surface during some stage ofgrowth (data not shown). The cytotoxic effect of SEAM 3 was observed oneach cell type (SK-MEL-28 melanoma, CHP-134 neuroblastoma, and Jurkatcells) and was approximately proportional to the level of antigenpresent on the cell surface.

Example 11 SEAM 3 Binding to Formalin-Fixed Paraffin Embedded TissuesSections from Human Tumors

Initial immunohistochemical analysis of antigens recognized by SEAM 3was performed on unfixed tissues out of concern that the de-N-acetylamino groups could be blocked by reaction with formaldehyde (videsupra). Subsequently, it was determined that the amino group inde-N-acetyl sialic acid is relatively unreactive as a result of itsclose proximity to the C1 carboxyl group. Therefore, large scalescreening of human tumors for the presence of SEAM 3-reactive antigenswas performed using formalin-fixed paraffin embedded tissue sectionssince processing the samples by this method considerably improves thepreservation of cell structural features.

Human tissue microarrays were obtained from US BioMax (Rockville, Md.).The tissue microarrays were deparaffinized in xylene (2 changes, 10minutes each) then rehydrated by sequential 5 minute washes in 100%ethanol, 95% ethanol, 70% ethanol, 50% ethanol, and PBS buffer.Endogenous peroxidase was blocked by incubation with Peroxidazed 1solution (Biocare, Concord, Calif.) for 5 minutes at ambienttemperature. The sections were blocked with Terminator (Biocare)containing streptavidin then rinsed with PBS buffer. The primaryantibody (purified SEAM 3 (vide infra), irrelevant IgG2b control, etc.at concentrations of 1 to 5 μg/ml)) was diluted in Da Vinci Greendilution buffer (Biocare) and incubated either overnight at 4 degrees C.or for 1 hour at ambient temperature. The slides were washed 3 times for10 minutes each with PBS buffer then incubated with biotin conjugatedrabbit anti-mouse IgG secondary antibody (5 μg/ml, Vector Labs,Burlingame, Calif.) for 30 minutes at ambient temperature. After washing3 times for 10 minutes each with PBS buffer, horse radishperoxidase-streptavidin conjugate (Vector Labs) was added and incubatedat ambient temperature for 30 minutes. The slides were washed 3 timesfor 10 minutes each with PBS buffer and incubated with AEC substrate(Vector Labs) containing hydrogen peroxide for color development. Colordevelopment was allowed to proceed for 30 seconds to 30 minutesdepending on the sample and was then stopped by washing with water,counter stained with Hematoxylin QS (Vector Labs), rinsed with water andfinally mounted in VectraMount AQ aqueous mounting medium (Vector Labs)and viewed/photographed under a microscope (Zeiss Axioplan).

The results for 47 human tumors are summarized in FIG. 40. All tumorsand normal tissues tested were negative for binding with the irrelevantisotype-matched control mAb (murine IgG2b, Southern Biotech). Theintensity of staining and the number of cells stained was variable inthe tumor samples ranging form no staining to (indicated by “−”) to darkstaining of all cells (indicated by “+++”) with variations between theextremes. Most of the tumor samples tested were positive for SEAM 3binding (38 of 47) and represent a broad range of tumor types.Typically, the staining resulting from SEAM 3 binding observed in thetumor tissues has a “granular” appearance and is coincident with cellstructures. A micro array of normal tissues was also tested. Generally,the “normal” tissue samples were obtained from the same subjects as thetumors but were obtained from regions outside the margins of the primarytumors. All of the normal tissues (17 samples) were negative for bindingwith the control mAb. SEAM 3 was positive for binding to 15 of 17samples ranging from +to ++. However, unlike the staining observed intumor tissues, staining resulting from SEAM 3 binding in the normaltissues is not granular but is instead homogenous, is not coincidentwith cell structures except for a few cells, and is continuous withstromal tissues. At the present time the differences in the appearanceof staining is not understood.

Example 12 SEAM 3 Binding to Human Melanoma SK-MEL-28, and NeuroblastomaCHP-134 Cell Lines by Fluorescence Microscopy and Flow Cytometry

SK-MEL-28 cells (Carey et al. Proc Natl Acad Sci USA, 1976. 73(9):3278-82) cells were purchased from the American Type Culture Collection(ATCC). Cells were grown routinely in RPMI 1640 medium containing 0.1 mMnon-essential amino acids, 1.0 mM sodium pyruvate, 0.1 mM glutamate,penicillin/streptomycin and 10% fetal bovine serum at 37° C. in 95%air:5% C0₂. Confluent cells were sub-cultured (1:3 to 1:8) by treatingwith 0.25% (w/v) Trypsin/0.53 mM EDTA solution, washed and trituratedbefore re-seeded into new growth medium. SK-Mel 28 cells were only usedup to passage 10 from the ATCC stock cells. These cells express theganglioside GD3.

The human T cell leukemia cell line Jurkat (Schneider et al. Int JCancer, 1977. 19(5):; Schneider et al. Haematol Blood Transfus, 1977.20:) were grown in RPMI 1640 containing 10% FBS, 2 mM L-glutamine in 5%CO2 at 37° C. and subcultured every 3 days with a split ratio of about1:5. Cells were collected by centrifugation (500g) and resuspended infresh medium before subculture. The cells are positive for expression ofthe following CD antigens: CD2, CD3, CD4, CDS, CD6, CD7, CD34, and arenegative for expression of CD8, CD13, CD19, TCRalpha/beta,TCRgamma/delta.

CHP-134 neuroblastoma cells (Livingston et al. J Biol Chem, 1988.263(19):. 9443-8) were routinely grown in RPMI 1640 medium containing0.1 mM non-essential amino acids, 1.0 mM sodium pyruvate, 0.1 mMglutamate, penicillin/streptomycin and 10% fetal bovine serum at 37° C.in 95% air:5% CO₂. Confluent cells were sub-cultured (1:3 to 1:5) bytreating with Cell Dispersal Reagent (CDR, Guava Technologies, Haywood,Calif.), washed and trituated before re-seeded into new growth medium.These cells express the neural cell adhesion molecule (NCAM) which ismodified with long chain polysialic acid (i.e. poly alpha 2-8 N-acetylneuraminic acid).

To observe binding of SEAM 3 to the surface of cells, adherent CHP-134or SK-Mel-28 cells (approximately 10⁵ cells) were cultured on multi-wellmicroscope slides that had been treated with ploy-L-lysine (Nunc). Afteran overnight incubation cells were gently washed with PBS buffer andfixed with ice-cold 1% (v/v) formaldehyde. After 20 minutes cells werewashed with PBS before blocking non-specific binding with a solution of3% goat serum for 1 hour. To observe the presence of SEAM 3-reactiveantigen that is present inside the cells, the cells were treated TritonX-100 0.5% w/v in 3% goat serum for 1 hour. The primary antibodies wereadded and incubated for 2 hours or overnight at 4° C. Cells were gentlywashed by a series (at least twice) with ice-cold PBS beforeisotype-specific secondary antibody (produced in goat) conjugated witheither Alexa Fluor 488 (immunofluorescence and confocal), Alexa Fluor546 (confocal) Alexa Fluor 594 (immunofluorescence), Alexa Fluor 633(confocal) was applied for at least 1 hour at 4° C. in the dark (allsecondary antibodies conjugated to fluorophores were obtained fromInvitrogen, Carlsbad, Calif.). After another series of gentle washes, ahardening mounting medium containing DAPI was applied.

Immunofluorescence was observed with a Zeiss Axioplan FluorescenceMicroscope fitted with a digital camera. Confocal images were obtainedusing a Zeiss Meta510 CLSM at the Biological Imaging Facility,University of California, Berkeley, Calif. and were analyzed usingImageJ Software (NIH). Control antibodies and secondary antibodiesapplied alone were routinely used to assess background fluorescence. Thepositive control mAb that is specific for GD3, R24 was positive forbinding to SK-MEL-28 melanoma cells but negative for binding to CHP-134neuroblastoma (Livingston et al. J Biol Chem, 1988. 263(19): 9443-8) andJurkat T-cell leukemia cells, which do not express GD3 (data not shown).

FIG. 41 and FIG. 42 show fluorescence on the cell surface (dark shadingin the figure) resulting from SEAM 3 binding to SK-MEL-28 melanoma cellsand CHP-134 cells as measured by confocal microscopy. FIG. 43 shows SEAM3 binding to Jurkat cells as measured by fluorescence microscopy. Ineach case, the fluorescence is uniform over the cell surface. However,not all of the cells in the visual field show SEAM 3 binding. Foradherent SK-MEL 28 and CHP-134 cells, cells that are positive for SEAM 3binding differ morphologically from SEAM 3-negative cells. Positivecells are rounded up while negative cells are elongated. Usingtime-lapse photography of SK-MEL-28 cells in culture (at 37° C.,95%air:5% CO2), it was confirmed that the rounded up cells were not deadcells, but cells undergoing cell division. The cells remained in thespherical shape for approximately 3 hours, before they split into twodaughter cells.

It should be noted that SK-Mel-28 cells overexpress GD3 ganglioside andare positive for binding by the anti-GD3 mAb R24. CHP-134 cells are GD3negative, and are not bound by the R24 mAb. Moreover, since CHP-134cells do not express GD3, they also do not produce any de-N-acetylatedGD3 derivative. Since SEAM 3 binds to both SK-Mel-28 cells and CHP-134cells (and in fact exhibits greater binding to CHP-134 cells), thesedata indicate that SEAM 3 binds an antigen other than GD3 or GD3derivative. In addition, SEAM 3 does not bind to an antigen derived frompolysialic acid since it binds to SK-MEL-28 cells, which do not expressN-CAM. Therefore, SEAM 3 binds to an antigen other than GD3 or N-CAM.

Example 13 SEAM 3 Binding to SK-MEL 28 Melanoma, Jurkat T-Cell Leukemia,and CHP-134 Neuroblastoma Cells Measured by Flow Cytometry

Cells (approximately 10⁵ per well) were plated onto a flat bottom96-well tissue culture plate (Nunc) and incubated with growth mediumovernight before assay. Cells were detached from the plate by eithertrypsin (SK-MEL-28) or CDR (CHP-134) before being collected into a96-round bottom plate, spun at 500g for 5 minutes and fixed withice-cold 1% (v/v) formaldehyde. After 20 minutes cells were pelleted bycentrifugation (above) and incubated a blocking solution of 3% (v/v)goat serum with and without Triton X-100 (0.5% w/v) for 1 hour. Afterwhich the primary antibodies were added and incubated for 2 h orovernight at 4° C. The cells were washed twice by pelleting andresuspension in ice-cold PBS. Secondary antibody (Invitrogen, asdescribed above) was incubated with the cells for at least 1 hour at 4°C. in the dark. After another series of spins and washes (3 times)binding was analyzed by a Guava EastCyte flow cytometer. Control sampleswere treated with an isotype matched irrelevant antibody (SouthernBiotech), which were used to create baseline fluorescence, or positivecontrol mAbs that are reactive with antigens specifically expressed bythe cells (i.e. anti-GD3 for SK-MEL 28 cells and anti-NCAM in CHP-134cells). In addition, specificity of binding was shown for the Jurkatcells by preincubating SEAM 3 with 50 μg/ml N—Pr NmB PS prior to addingthe mAb to the cells.

As shown in FIGS. 44-46, SEAM 3 binds to the surface of all three celllines (-Triton). The greatest amount of binding was observed for theCHP-134 cells (FIG. 45) and the least in Jurkat cells (FIG. 46),although binding to Jurkat cells was still significant. All three celllines contain larger amounts of internal SEAM 3-reactive antigen(+Triton).

Example 14 Effect of SEAM 3 Binding on the Viability of Cancer Cells

Cell viability of SK-MEL 28 cells incubated in the presence of SEAM 3 orcontrol mAbs (irrelevant isotype IgG2b or anti-GD3, R24) was determinedusing ViaCount Reagent (Guava Technologies, Hayward, Calif.), as permanufacturers instructions. Briefly, cells that had been incubated withthe mAbs for 48 h were cleaved form the tissue culture plate (asdescribed above for the binding assays), collected by centrifugation andresuspended in ViaCount Reagent. The viability was analysed using apre-set program on the Guava EasyCyte flowcytometer. The program has apreset gate for apoptosis and this was routinely incorporated into ourstudies. As shown in FIG. 47, SEAM 3 significantly decreases the numberof viable cells compared to the irrelevant IgG2b control mAb (P<0.001indicated ***) after 24 h incubation with the mAb. In a secondexperiment shown in FIG. 48, SEAM 3 decreases the number of viable cellscompared to an IgG2b control mAb (P<0.05 indicated by *) and increasesthe number of apoptotic (P<0.05) and dead cells (P<0.01). Similarly, thepositive control mAb, R24 decreases the number of viable cells (P<0.01indicated **), and increases the number of apoptotic (P<0.01) and dead(P<0.001) cells compared to the negative control. The resultsdemonstrate that SEAM 3 binding to the cell surface induces apoptosisand increases cell death.

Example 15 Correlation Between SEAM 3 BInding and Cell Proliferation asMeasured by the Expression Of KI-67 Antigen

The data above indicated that SEAM 3 binds to the surface of cancercells that are in some stage of cell division. To demonstrate this,SK-MEL 28 cells were analyzed for SEAM 3 binding and for the expressionKi-67 antigen, which is a marker for cell proliferation (Brown et al.Histopathology. 2002, 40:2-11). Cells were processed by the sameprocedures used to measure SEAM 3 binding in the absence of Triton.After unbound SEAM 3 had been washed away, cells were treated with 3%(v/v) goat serum containing 0.5% Triton to allow entry of an anti-Ki-67antibody. After 1 h at 4° C., an anti-Ki-67 was added and incubatedon-ice for 2 hours. Cells were then collected by centrifugation, washedtwice with PBS, and two fluorescently labeled goat anti-mouse secondaryantibodies were added, anti IgG2b-Alexa Flour 594 (Invitrogen);anti-IgM-Alexa Flour 488 (Invitrogen). After extensive washing, cellswere analyzed on a Guava EasyCyte flow cytometer.

When the cells are in exponential growth phase, approximately 20% of thecells were found to express SEAM 3-reactive antigen on their surface (byflow cytometry and fluorescence microscopy data) and 20-25% express theproliferation marker Ki-67 (by flow cytometry). As shown in FIG. 50,there is a population of cells (approximately 11%) that express bothKi-67 and SEAM 3-reactive antigen on their surface. However, there aresome cells that only express Ki-67 antigen (12%) or SEAM 3-reactiveantigen (13%). Detection of Ki-67 antigen maybe used to determine thepercentage of tumor cells that are actively dividing in samples ofcancer biopsies (Brown et al. Histopathology. 2002, 40:2-11). The numberobtained through this examination is termed the “S-phase”, growth, orproliferative fraction (Brown et al. Histopathology. 2002, 40:2-11).Indeed, Ki-67 is present throughout proliferation from “S-phase to atleast anaphase. The flow cytometry double labeling experiment (FIG. 50)shows that the expression of Ki-67 and SEAM 3-reactive antigen on thesurface of cells overlap and confirm that at least in some part, SEAM3-reative antigen expression on the surface maybe involved in some latestage of cell division.

To further assess the affect of SEAM 3 mAb on cell growth, the stage ofthe cell cycle after treatment with SEAM 3 was determined. In thisexperiment, the cells were stained with the fluorescent DNA binding dyepropidium iodide to characterize cell populations in various stages ofthe cell cycle and the effects of adding control antibodies, nocodazole(a drug that arrest the cells in mitosis) and SEAM 3.

Approximately 10⁵ SK-MEL 28 cells were plated on a 96-well tissueculture plate and allowed to adhere. After 24 h the medium was replacedwith one that had either antibody or drug and incubated for a further 48h. Cells were spun (to collect any cells that may have detached), andfixed in 70% ice-cold methanol (added drop wise) for at least 30 minutesat 4° C. The cells were washed twice with PBS, and to ensure that onlyDNA was stained, the fixed cells were treated with ribonuclease I (100μg/ml, source) for 30 minutes at 37° C. Propidium iodide (50 μg/ml) wasadded and samples were analyzed using a Guava EasyCyte flow cytometer.

As shown in FIG. 49, the cells incubated for 48 h with anisotype-matched control antibody exhibited a profile where the majorityof the cells (68%) were in Go, or at rest (non-proliferating), while 10%were in “S-phase” and a further 15% in G2/M phase. A further population(approximately 10%) of cells were in a pre-Go phase. This pre-Go phasemay be indicative of apoptosis. SK-MEL-28 cells could be arrested inG2/M phase (mitosis) by treatment with nocodazole (100 nM) for 48 h(FIG. 49). In this case, approximately 50% of the cells were arrested inG2/M phase. In contrast, incubation of the cells with SEAM 3 reduced theproportion of cells in Go, S-phase and G2/M Phase, while increasing thenumber in pre-Go (FIG. 49).

This data provides further evidence that SEAM 3 decreases the viabilityof SK-MEL 28 cells and suggests that the effect of the antibody is topromote entry of the cells into the pre-Go phase. Interestingly, thecells that had been treated with the anti-ganglioside GD3 antibody(R24), which has previously been shown to kill melanoma cells, increasedthe number of cells in mitosis. Thus, the mechanism(s) of action of SEAM3 on interrupting cell cycle/apoptotic mechanisms may be different fromthose exhibited by R24. In addition, this difference in the effect oncell cycle is further evidence that SEAM 3 and R24 bind differentepitopes on cancerous cells.

Example 16 Cloning and Sequencing of Nucleic Acid Encoding the SEAM 3MAB

To investigate the molecular basis for antigen recognition, the variableregion (V) genes of five anti-N—Pr NmB PS murine mAbs that arebactericidal for N. meningitidis Group B bacteria were cloned andsequenced. The following materials and methods were used in thisexample.

Methods and Materials

mAbs The anti-N—Pr NmB PS murine mAbs SEAM 2 (IgG3), SEAM 3 (IgG2b),SEAM 12 (IgG2a), SEAM 18 (IgG2a) are representative of each of the fourfine antigenic specificity groups described previously (Granoff et al.(1998) J Immunol 160, 5028-36). SEAM 35 (IgG2a) also was includedbecause it exhibits greater cross-reactivity with polysialic acidantigens expressed by the human neuronal cell line CHP-134 than that ofthe other four SEAM mAbs. The mAbs are bactericidal in the presence ofcomplement and confer passive protection against meningococcalbacteremia in an infant rat model. SEAM 2 and SEAM 3 have no detectableautoreactive activity with host polysialic acid while SEAM 12 and SEAM18 show minimal cross-reactivity.

dsDNA ELISA. mAb binding to dsDNA was measured using methods describedby Gilkeson et al. (1993) J Immunol 151, 1353-64. The positive controlanti-DNA mAb was obtained from QED Biosciences (San Diego, Calif.) andisotype-matched irrelevant mAbs were obtained from Southern Biotech Inc.(Birmingham, Ala.).

V gene sequencing. Variable region genes of immunoglobulin heavy andlight chains from mouse hybridoma cell lines were amplified by PCR usingdegenerate primers and cloned into the vector pGEM3zf (Promega, Madison,Wis.) as described by Wang et al. (2000) J Immunol Methods 233, 167-77using E. coli strain XL-2 Blue as a host. Plasmid DNA from individualtransformants selected on LB-ampicillin plates was isolated using theQiagen Mini Prep Kit (Qiagen) according to the manufacturersinstructions. The cloned V genes were sequenced by BioNexus (Oakland,Calif.).

V gene sequence analysis. The mAb nucleotide sequences were analyzedusing IGMT/V-QUEST and the mouse immunoglobulin nucleotide sequencedata-base through the online web facilities of the internationalImMunoGeneTics® information system (IMGT, on the internet atimgt.cines.fr) that was initiated and coordinated by Marie-Paule Lefranc(Université Montpellier II, CNRS, LIGM, IGH, IFR3, Montpellier, France).Putative germline genes were selected based on the closest match betweengermline sequence in the database and cloned V gene sequence. Both aminoacid and gene sequences were compared to respective sequences in theGenBank non-redundant sequence databases using BLAST (Altschul et al.(1997) Nucleic Acids Res 25, 3389-402). In addition, putative germlinegenes used by a hybridoma clone expressing the anti-NmB PS murine mAb,735 (IgG2a) were identified from the literature. Since only the aminoacid sequence of this mAb was available (Klebert et al. 1993 Biol ChemHoppe Seyler 374, 993-1000; Vaesen et al. (1991) Biol Chem Hoppe Seyler372, 451-3), the predicted germline gene for this mAb is based on theclosest amino acid sequence match in the IGMT/V-QUEST and GenBank/EMBLdatabases (Chenna et al. (2003) Nucleic Acids Res 31, 3497-500). We alsoincluded in our comparative analysis the gene sequences and germlinegene assignments for the anti-NmB PS mAb 2-2-B (IgM, Mandrell et al.(1982) J Immunol 129, 2172-8) reported by Berry et al. ((2005) MolImmunol 42, 335-44).

Results

Analysis of nucleic acid and amino acid sequences of variable regions ofSEAM 3 heavy chain and light chain polypeptides. The nucleic acid andamino acid sequences of the variable regions of the SEAM 3 heavy chainpolypeptide and light chain polypeptide are provided in FIG. 51. FIGS.52 and 53 show the SEAM 3 light chain and heavy chain variable regionDNA sequences, respectively, with the framework (denoted by, e.g., FR1-IMTG; FIG. 56-58) and CDR regions indicated as defined by theInternational Immunogenetics Information System (IMGT) definitions(Lefranc et al. IMGT, the international ImMunoGeneTics informationsystem®. Nucl. Acids Res., 2005, 33, D593-D597).

Variable region gene usage of murine anti-N—Pr NmB PS mAbs The germlinegene usage for the anti-N—Pr NmB PS and anti-NmB PS mAbs are compared inthe table provided in FIG. 55. The respective amino acid sequences areshown in FIGS. 50 and 51. The V region repertoire is restricted to arelatively few highly related VL or VH gene families. For example, SEAM2 and SEAM 3, which have different fine antigenic specificities, haveidentical VL amino acid sequences (FIG. 52), and the VL gene is from thesame family gene family (IgGKV1) as that encoding the autoreactiveanti-NmB PS mAbs, 2-2-B and 735 (FIG. 55). Similarly, the VL genes usedby SEAM 12 and SEAM 18, which have different fine antigenicspecificities, are from the same family (IgGKV4). The respective VHsequences of SEAM 3 and SEAM 18 are nearly identical to each other (96%identity), and are from the same germline gene family (IgGHV7S3) usedfor SEAM 35 VH (FIG. 55). The germline VH genes for SEAM 2 and SEAM 12are different from each other and from the other three anti-N—Pr NmB PSmAbs but the germline VH gene used for SEAM 2 is related to those usedby the two autoreactive anti-NmB PS mAbs, 2-2-B and 735 (both 72%identical).

Anti-NmB PS mAbs, 2-2-B and 735 are reactive with NmB PS while anti-N PrNmB PS SEAM 2 is not. The close homology of both the respective heavyand light chain V amino acid sequences between SEAM 2 and theautoreactive mAbs 2-2-B and 735 (VH 70%, VL 75%), is therefore ofparticular interest. The most striking difference between the twosequences is in the heavy chain (H—CDR3) where SEAM 2 consists of theminimal 4 amino acids, two of which are glycine, compared with a lengthof 8 amino acids in mAb 735.

The VL and VH genes of anti-NmB PS mAb 2-2-B are unmutated (100%identical) as compared with their putative germline genes (FIG. 55).Similarly, the amino acid sequence of the expressed VL of anti-NmB PSmAb 735 is >99% identical to that of the assigned germline gene. Incontrast, the anti-N—Pr NmB PS mAbs have a greater percentage ofmutations as compared with the respective germline sequences (theexpressed genes are 89% to 95% identical to germline sequences, FIG.55). Also, all five anti-N—Pr NmB PS mAbs contain one or more arginineresidues in H—CD3, which are encoded by editing at the D-J junction.Neither of the two anti-NmB PS mAbs contain arginine in H—CDR3.

1.-44. (canceled)
 45. An antibody that specifically binds ade-N-acetylated sialic acid (deNAc SA) epitope on an extracellularlyaccessible surface of a cancerous cell, the deNAc SA epitope minimallydefined by a dimer containing at least one de-N-acetylated sialic acidresidue having a free amine adjacent an N-acylated sialic acid residueor a sialic acid derivative residue, wherein: the antibody binds to thedeNAc SA epitope on the surface of CHP-134 neuroblastoma cells, and theantibody competes for binding to the deNAc SA epitope with an antibodycomprising: a heavy chain polypeptide comprising: a VH CDR1 comprisingamino acid residues 26 to 35 of SEQ ID NO:7, a VH CDR2 comprising aminoacid residues 50 to 66 of SEQ ID NO:7, a VH CDR3 comprising amino acidresidues 101 to 108 of SEQ ID NO:7; and a light chain polypeptidecomprising: a VL CDR1 comprising amino acid residues 24 to 39 of SEQ IDNO:3, a VL CDR2 comprising amino acid residues 55 to 61 of SEQ ID NO:3,and a VL CDR3 comprising amino acid residues 94 to 100 of SEQ ID NO:3.46. The antibody of claim 45, wherein the antibody is selected from thegroup consisting of: an IgG, a F(ab′)2, a F(ab), an Fv, or an scFv. 47.The antibody of claim 45, wherein the antibody is a humanized antibodyor a fully human antibody.
 48. The antibody of claim 45, wherein theantibody comprises: a heavy chain polypeptide comprising: a VH CDR1comprising amino acid residues 26 to 35 of SEQ ID NO:7, a VH CDR2comprising amino acid residues 50 to 66 of SEQ ID NO:7, and a VH CDR3comprising amino acid residues 101 to 108 of SEQ ID NO:7; and a lightchain polypeptide comprising: a VL CDR1 comprising amino acid residues24 to 39 of SEQ ID NO:3, a VL CDR2 comprising amino acid residues 55 to61 of SEQ ID NO:3, and a VL CDR3 comprising amino acid residues 94 to100 of SEQ ID NO:3.
 49. The antibody of claim 45, wherein the deNAc SAepitope is presented on a surface of the cancerous cell during celldivision.
 50. The antibody of claim 45, wherein the cancerous cell is amelanoma cell or a leukemia cell.
 51. The antibody of claim 45, whereinthe cancerous cell is a neuroblastoma cell.
 52. A nucleic acid encodingone or more chains of the antibody of claim
 45. 53. An expression vectorcomprising the nucleic acid of claim
 52. 54. A recombinant host cellcomprising the expression vector of claim
 53. 55. A recombinant hostcell comprising the antibody of claim
 45. 56. A pharmaceuticalcomposition, comprising: the antibody of claim 45; and apharmaceutically acceptable carrier.
 57. A method of inhibiting growthof a cancerous cell in a subject, wherein an extracellularly accessiblesurface of the cancerous cell comprises a deNAc SA epitope minimallydefined by a dimer containing at least one de-N-acetylated sialic acidresidue having a free amine adjacent an N-acylated sialic acid residueor a sialic acid derivative residue, the method comprising:administering to a subject a pharmaceutically-acceptable formulationcomprising the antibody of claim 45, wherein said administeringfacilitates reduction in viability of cancerous cells bound by theantibody.
 58. The method of claim 57, wherein the deNAc SA epitope ispresented on a surface of the cancerous cell during cell division. 59.The method of claim 57, wherein the cancerous cell is a melanoma cell ora leukemia cell.
 60. The method of claim 57, wherein the cancerous cellis a neuroblastoma cell.
 61. The method of claim 57, wherein theantibody is administered by infusion or by local injection.
 62. Themethod of claim 57, wherein said administering is prior to, at the timeof, or after surgical intervention to remove cancerous cells from thesubject.
 63. The method of claim 57, further comprising administering atleast one of a cancer chemotherapy or a radiation therapy to thesubject.
 64. A method of detecting a tumor in a subject, the methodcomprising: contacting a biological sample obtained from a subjectsuspected of having cancer with the antibody of claim 45, saidcontacting being under conditions suitable for specific binding of theantibody to a deNAc SA epitope in the biological sample; wherein thepresence or absence of binding of the antibody is indicative of thepresence or absence of cancerous cells having a cell surface deNAc SAepitope in the subject.